DarwinOmics.ai

Executable analysis tools and native computational steps

Tools

QC, trimming, alignment, quantification, differential analysis, annotation, variant calling, proteomics, microbiome, image, and matrix operations with captured inputs, parameters, outputs, and provenance.

FastQCSTARSalmonDESeq2GATKSAMtools
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3DFlex 3DFlex runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool ADMIXTOOLS2 ADMIXTOOLS2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Admixture Admixture runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Aggrescan3d Aggrescan3d runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Aldy Aldy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Alevin Fry Alevin Fry runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool COMBINE-lab/salmon | 901 stars Allen Brain Sdk Allen Brain Sdk runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Alphamissense Db Alphamissense Db runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool google-deepmind/alphafold | 14,697 stars Alphapept Alphapept runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Alphapeptstats Alphapeptstats runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ambertools Ambertools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ancom Bc Ancom Bc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Annotate Variants Annotates VCF variants with gene names, functional consequences, population frequencies, and clinical significance. Uses gene models and variant databases. Tools Runnable aligned sequencing reads Annovar Annovar supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Tools Runnable Analysis tool Archr Archr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ascat Ascat runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Auspice Auspice runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Autodock Vina Autodock Vina runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Autopvs1 Autopvs1 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bagel2 Bagel2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bakta Annotate bacterial genomes using Bakta. Tools Runnable Analysis tool Bayesspace Bayesspace runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bbknn Bbknn runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bcftools View, filter, and manipulate VCF/BCF variant files. Tools Runnable Analysis tool samtools/bcftools | 875 stars Beagle5 Beagle5 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bedtools Performs interval operations on genomic data: intersect, subtract, closest, merge, sort. Use to find peaks overlapping genes, annotate variants with gene names, or merge overlapping intervals. Tools Runnable Analysis tool Big Fish Big Fish processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Binseq Binseq runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bioconductor Ecosystem Bioconductor Ecosystem runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bioimageio Runner Bioimageio Runner processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Bismark Call methylation from bisulfite sequencing using Bismark. Tools Runnable aligned sequencing reads Bismark Align Bismark aligns bisulfite-converted reads for methylation analysis. Handles C->T conversion specific to bisulfite sequencing. Use for WGBS and RRBS data. Tools Runnable sequencing reads Blast Search sequences against databases using BLAST. Tools Runnable Analysis tool Blast Plus Blast Plus runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bolt Lmm Bolt Lmm runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bowtie2 Align short reads to reference using Bowtie2. Tools Runnable sequencing reads BenLangmead/bowtie2 | 795 stars Bowtie2 Align Bowtie2 aligns short DNA reads to a reference genome. Commonly used for ChIP-seq, ATAC-seq, and other short-read DNA assays. Does NOT handle spliced alignments. Tools Runnable sequencing reads BenLangmead/bowtie2 | 795 stars Bracken Estimate species abundance from Kraken2 output. Tools Runnable sequencing reads Brainlife Brainlife runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Brainsmash Brainsmash runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Brainsuite Brainsuite runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Breedr Breedr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Brms R Brms R runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Busco Busco runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Bwa Align DNA reads to a reference genome using BWA-MEM algorithm. Tools Runnable Analysis tool lh3/bwa | 1,753 stars Bwa Mem BWA-MEM aligns DNA sequencing reads to a reference genome. Standard aligner for WGS, WES, ChIP-seq, and ATAC-seq. Does NOT handle spliced alignments - use STAR or HISAT2 for RNA-seq. Only ~4GB RAM for human genome. Tools Runnable sequencing reads lh3/bwa | 1,753 stars Bwa Mem2 BWA-MEM2 is a faster version of BWA-MEM producing nearly identical results. 1.5-2x faster. Use when you have DNA-seq data and want faster alignment. Requires SSE4.2 CPU support. Tools Runnable sequencing reads lh3/bwa | 1,753 stars Cafe5 Cafe5 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cassavabase Tools Cassavabase Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Celloracle Celloracle runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cellprofiler Cellprofiler processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Cellranger Count CellRanger counts gene expression from 10x Genomics single-cell data. Handles cell barcode detection, UMI counting, and gene-cell matrix generation. Requires 10x-specific FASTQ naming. Tools Runnable sequencing reads Cellrank Traj Cellrank Traj runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cellrank2 Cellrank2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Celltag Celltag runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cellxgene Cellxgene runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Chimerax Chimerax runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Chopper Chopper runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Chromap Chromap runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Chromvar Chromvar runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cibersortx Cibersortx runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Civic Civic runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Clustergrammer2 Clustergrammer2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Clusterprofiler Clusterprofiler runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cnvkit Detect copy number variants from targeted sequencing. Tools Runnable Analysis tool Cobrapy Cobrapy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Coloc Coloc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Comet Comet runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Compass Compass runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Complexa Evaluate Pdbs Complexa Evaluate Pdbs applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data NVIDIA-BioNeMo/bionemo-recipes | 806 stars Complexa Setup Complexa Setup runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool NVIDIA-BioNeMo/bionemo-recipes | 806 stars Complexa Target Complexa Target applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data NVIDIA-BioNeMo/bionemo-recipes | 806 stars Compound Discoverer Compound Discoverer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Control Freec Control Freec runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Controlfreec Controlfreec runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cooltools Cooltools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Count Matrix Builds a gene count matrix from aligned reads and gene annotations. Combines featureCounts output from multiple samples into a single matrix for differential expression analysis. Tools Runnable expression matrices Cpic API Cpic API runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cpic API V2 Cpic API V2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Crispr Prediction Crispr Prediction runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cromwell Wdl Runner Cromwell Wdl Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sample metadata Cropsr Cropsr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cryosparc Cryosparc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cryosparc V4 Cryosparc V4 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cutadapt Research-certified Rust-native Cutadapt 5.2-compatible exact adapter trimming for research data artifact. Tools Runnable sequencing reads marcelm/cutadapt | 582 stars Cutandrun Tools Cutandrun Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Cwl Runner Cwl Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sample metadata Cytoscape Desktop Cytoscape Desktop runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool cytoscape/cytoscape.js | 11,069 stars Dandelion Dandelion runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Candidate Ranker Darwinomics Candidate Ranker runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Cert Agent Callability Runner Darwinomics Cert Agent Callability Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Cert Fixture Oracle Runner Darwinomics Cert Fixture Oracle Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Cert No Simulation Audit Darwinomics Cert No Simulation Audit runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Cert Provider Live Validation Darwinomics Cert Provider Live Validation runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Cert Research Grade Biology Module cert research grade biology module Tools Runnable Analysis tool Darwinomics Cgt Assay Manifest Validate Checks assay manifest completeness, sample identifiers, declared assays, and provenance fields. Tools Available sample metadata Darwinomics Cgt Audit Trail Export Exports audit trail records from CGT research data artifact manifests and provenance metadata. Tools Available Analysis tool Darwinomics Cgt Base Prime Editing Readout Summarizes base-editing or prime-editing readouts from aligned sequencing evidence. Tools Available aligned sequencing reads Darwinomics Cgt Batch Release Decision Support Compares release specifications and available evidence to produce release decision support rows. Tools Available Analysis tool Darwinomics Cgt Biodistribution Shedding Summary Summarizes biodistribution and shedding measurement tables into safety signal rows. Tools Available Analysis tool Darwinomics Cgt Biosafety Review Package Builds biosafety review package rows from safety signals and supporting evidence. Tools Available Analysis tool Darwinomics Cgt Bulk RNA-seq Expression Profile Summarizes bulk RNA-seq expression evidence into CGT expression profile rows. Tools Available expression matrices Darwinomics Cgt Cell Expansion Kinetics Transforms cell expansion measurements into growth and process trend rows. Tools Available Analysis tool Darwinomics Cgt Cell Source Characterization Characterizes source-cell composition, identity, and state from single-cell evidence. Tools Available Analysis tool Darwinomics Cgt Cell State Comparability Map Compares cell product state profiles across lots, processes, or timepoints. Tools Available Analysis tool Darwinomics Cgt Cell Viability Count QC Normalizes cell count, viability, and recovery measurements into QC metric rows. Tools Available Analysis tool Darwinomics Cgt Chain Of Custody Ledger Normalizes chain-of-custody events for collection, manufacturing, testing, shipment, and administration milestones. Tools Available Analysis tool Darwinomics Cgt Chain Of Identity Register Creates chain-of-identity records linking subject, collection, product, and study identifiers. Tools Available Analysis tool Darwinomics Cgt Cmc Design Control Trace Builds design-control traceability rows across target evidence, construct versions, and CMC specifications. Tools Available Analysis tool Darwinomics Cgt Comparability Protocol Plan Creates comparability analysis plans from CQA maps and declared study context. Tools Available Analysis tool Darwinomics Cgt Comparability Statistical Analysis Computes comparability summaries from planned metrics and available product evidence. Tools Available Analysis tool Darwinomics Cgt Consent Eligibility Map Maps study criteria, consent metadata, and subject attributes into eligibility evidence rows. Tools Available Analysis tool Darwinomics Cgt Construct Design Spec Transforms target evidence into structured therapeutic construct design specifications. Tools Available Analysis tool Darwinomics Cgt Construct Release Spec Compile Compiles construct-specific release specifications and acceptance criteria into research data artifact rows. Tools Available Analysis tool Darwinomics Cgt Copy Number Vector QC Normalizes vector copy-number measurements into QC metrics and evidence rows. Tools Available Analysis tool Darwinomics Cgt Critical Quality Attribute Map Maps QC metrics to critical quality attributes, acceptance criteria, and supporting evidence. Tools Available Analysis tool Darwinomics Cgt Cytokine Release Panel Normalizes cytokine release panel measurements into safety signal rows. Tools Available Analysis tool Darwinomics Cgt Deviation Capa Linker Links validation findings to deviation, investigation, and CAPA quality event rows. Tools Available Analysis tool Darwinomics Cgt Editing Outcome Quantify Quantifies observed editing outcomes from aligned sequencing evidence and emits edit summary rows. Tools Available aligned sequencing reads Darwinomics Cgt Empty Full Capsid Analysis Summarizes empty, partial, and full capsid assay measurements as QC metrics. Tools Available Analysis tool Darwinomics Cgt Immunogenicity Risk Evidence Maps immunogenicity evidence records into safety signal research data artifact rows. Tools Available Analysis tool Darwinomics Cgt Insertional Mutagenesis Risk Summarizes integration-site evidence into insertional mutagenesis risk signal rows. Tools Available Analysis tool Darwinomics Cgt Kg Grounding Evidence Link Links CGT evidence records to BioKG nodes and edges for traceable grounding. Tools Available Analysis tool Darwinomics Cgt Long Term Followup Monitor Summarizes long-term follow-up observations, visit windows, and safety event continuity. Tools Available Analysis tool Darwinomics Cgt Metabolic State Profile Summarizes metabolic assay evidence into cell product state profile rows. Tools Available Analysis tool Darwinomics Cgt Nonviral Delivery Formulation QC Summarizes nonviral delivery formulation measurements as research data artifact QC metrics. Tools Available Analysis tool Darwinomics Cgt Offtarget Variant Annotate Annotates observed variant evidence for editing off-target risk assessment. Tools Available variant calls Darwinomics Cgt Process Parameter Trend Computes process parameter trend rows across vector or cell manufacturing runs. Tools Available Analysis tool Darwinomics Cgt Protocol Deviation Detect Compares manufacturing and assay records to protocol-defined expectations and emits validation findings. Tools Available Analysis tool Darwinomics Cgt Regulatory Evidence Pack Assembles CMC, safety, clinical, and quality evidence manifests into regulatory package rows. Tools Available Analysis tool Darwinomics Cgt Release Certificate Build Builds product release certificate rows from release decision and evidence metadata. Tools Available Analysis tool Darwinomics Cgt Replication Competent Virus QC Normalizes replication-competent virus assay evidence into QC metric rows. Tools Available Analysis tool Darwinomics Cgt Residual Host Cell DNA QC Normalizes residual host-cell DNA measurements into QC metrics and acceptance evidence. Tools Available Analysis tool Darwinomics Cgt Secretome Proteomics Profile Transforms secretome or proteomics measurements into product protein profile rows. Tools Available protein or structure data Darwinomics Cgt Singlecell Atac Accessibility Profile Transforms single-cell ATAC peak evidence into product epigenomic profile rows. Tools Available Analysis tool Darwinomics Cgt Singlecell Multiome Integrate Integrates declared single-cell RNA and chromatin evidence into multiome product profile rows. Tools Available Analysis tool Darwinomics Cgt Singlecell RNA-seq Profile Builds single-cell RNA-seq product profiles including cell identity, state, and metadata. Tools Available Analysis tool Darwinomics Cgt Sterility Mycoplasma QC Normalizes sterility and mycoplasma assay results into QC metric rows. Tools Available Analysis tool Darwinomics Cgt Study Intake Normalize Normalizes study-level CGT intake records into therapy, indication, sponsor, cohort, and provenance rows. Tools Available Analysis tool Darwinomics Cgt Tcr Car Expression Profile Summarizes TCR, CAR, or transgene expression evidence into product expression profile rows. Tools Available expression matrices Darwinomics Cgt Therapeutic Target Evidence Map Aggregates target rationale, disease biology, variant, expression, and literature evidence into target evidence rows. Tools Available Analysis tool Darwinomics Cgt Transduction Editing Efficiency QC Normalizes transduction or editing efficiency measurements into QC metrics. Tools Available Analysis tool Darwinomics Cgt Transgene Cassette Annotation Annotates transgene cassette features, coding regions, regulatory elements, and sequence provenance. Tools Available sequence data Darwinomics Cgt Tumorigenicity Risk Evidence Maps tumorigenicity evidence records into safety signal research data artifact rows. Tools Available Analysis tool Darwinomics Cgt Vdj Clonotype Profile Summarizes VDJ and clonotype evidence for immune cell therapy products. Tools Available Analysis tool Darwinomics Cgt Vector Backbone Annotation Annotates vector backbone sequence features and maps backbone evidence into research data artifact rows. Tools Available sequence data Darwinomics Cgt Vector Genome Titer QC Transforms vector genome titer measurements into QC metric rows with acceptance metadata. Tools Available Analysis tool Darwinomics Cgt Vector Identity QC Computes vector identity quality metrics from sequence or reference evidence. Tools Available sequence data Darwinomics Cgt Vector Potency QC Normalizes vector potency assay results into potency assay research data artifact rows. Tools Available Analysis tool Darwinomics Cgt Viral Integration Site Map Maps vector integration-site evidence from aligned reads into integration site rows. Tools Available aligned sequencing reads Darwinomics Compare Aligned Reads Research-certified deterministic compare_aligned_reads comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Assembled Contigs Research-certified deterministic compare_assembled_contigs comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Dcrf Auto Research-certified deterministic compare_dcrf_auto comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Differential Expression Research-certified deterministic compare_differential_expression comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Embedding Research-certified deterministic compare_embedding comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Expression Research-certified deterministic compare_expression comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Generic Normalize Research-certified deterministic compare_generic_normalize comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Genomic Intervals Research-certified deterministic compare_genomic_intervals comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Image Research-certified deterministic compare_image comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Image Segmentation Research-certified deterministic compare_image_segmentation comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Matrix Research-certified deterministic compare_matrix comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Peaks Research-certified deterministic compare_peaks comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Protein Sequence Research-certified deterministic compare_protein_sequence comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Protein Structure Research-certified deterministic compare_protein_structure comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare QC Metrics Research-certified deterministic compare_qc_metrics comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Raw File Research-certified deterministic compare_raw_file comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Reads Research-certified deterministic compare_reads comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Reads QC Research-certified deterministic compare_reads_qc comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Segmentation Research-certified deterministic compare_segmentation comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Sequence Research-certified deterministic compare_sequence comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Singlecell Research-certified deterministic compare_singlecell comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Tabular Research-certified deterministic compare_tabular comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Variant Annotations Research-certified deterministic compare_variant_annotations comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Variants Research-certified deterministic compare_variants comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Compare Visualization Research-certified deterministic compare_visualization comparison for research data artifact to research data artifact. Tools Runnable Analysis tool Darwinomics Dcrf Ingest Bulk materializes downloaded or uploaded data assets into normalized research data artifact artifact manifests before downstream analysis modules execute. Tools Runnable sample metadata Darwinomics Design Certification Gate Darwinomics Design Certification Gate runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Design Executor Darwinomics Design Executor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Design Manifest Indexer Darwinomics Design Manifest Indexer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Design Program Compiler Darwinomics Design Program Compiler runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Design Program Parser Darwinomics Design Program Parser runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Design Program Validator Darwinomics Design Program Validator runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Citation Extractor Darwinomics Doc Citation Extractor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Contract Dcrf Mapper doc analysis element dcrf mapper Tools Runnable Analysis tool Darwinomics Doc Contract Gap Analyzer doc analysis element gap analyzer Tools Runnable Analysis tool Darwinomics Doc Contract Normalizer Darwinomics Doc Contract Normalizer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Contract Validator Darwinomics Doc Contract Validator runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Evidence Ledger Darwinomics Doc Evidence Ledger supports differential analysis from expression matrices, preserving effect sizes, test statistics, and result tables for comparison. Tools Runnable Analysis tool Darwinomics Doc License Terms Extractor Darwinomics Doc License Terms Extractor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Methods Protocol Extractor Darwinomics Doc Methods Protocol Extractor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Model Card Reader Darwinomics Doc Model Card Reader runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Repo Readme Reader Darwinomics Doc Repo Readme Reader runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Research Certification Extractor Darwinomics Doc Research Certification Extractor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Table Figure Extractor Darwinomics Doc Table Figure Extractor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Doc Tool Entity Linker Darwinomics Doc Tool Entity Linker runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Bayesian Darwinomics Optimizer Bayesian runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Beam Search Darwinomics Optimizer Beam Search runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Evolutionary Darwinomics Optimizer Evolutionary runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Gradient Proxy Darwinomics Optimizer Gradient Proxy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Greedy Coordinate Darwinomics Optimizer Greedy Coordinate runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Mcmc Darwinomics Optimizer Mcmc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Nsga2 Darwinomics Optimizer Nsga2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Proto Stage Runner Darwinomics Optimizer Proto Stage Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Random Search Darwinomics Optimizer Random Search runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Optimizer Simulated Annealing Darwinomics Optimizer Simulated Annealing runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Paper Figure Diagram2graph Native Rust paper-figure diagram and pathway extractor for replication validation. Reads a single paper figure asset, emits structured node-edge or panel targets, and stays inside DarwinOmics research data artifact execution. Tools Available Analysis tool Darwinomics Paper Figure Scatteract Native Rust paper-figure scatter and volcano extractor for replication validation. Tools Available Analysis tool Darwinomics Paper Figure Source Acquirer Local Rust paper-figure source acquirer for replication validation. Resolves PubMed/PMC article pages, follows PMC figure pages, and emits figure image/caption sources with retrieval provenance for downstream plot parsing. Tools Catalog Analysis tool Darwinomics Paper Supplementary Material Extractor Extracts paper supplementary archives, spreadsheets, delimited tables, document tables, and optional Lift schema-guided PDF/table JSON into source-backed paper target evidence for deterministic validation. Tools Local Analysis tool Darwinomics Paper Target Extractor Deterministic paper-target extraction scaffold for replication validation. Converts paper URLs, request text, imported public-source metadata, and planned reproduction modules into a structured paper target specification without inventing... Tools Runnable Analysis tool Darwinomics Pareto Frontier Darwinomics Pareto Frontier runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Darwinomics Proto Gene Annotation Crispr Tracr RNA proto gene annotation crispr tracr rna Tools Runnable sequence data Darwinomics Proto Gene Annotation Meme Darwinomics Proto Gene Annotation Meme runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Gene Annotation Minced Darwinomics Proto Gene Annotation Minced runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Gene Annotation Miranda Darwinomics Proto Gene Annotation Miranda runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Gene Annotation Promoter Calculator proto gene annotation promoter calculator Tools Runnable sequence data Darwinomics Proto Gene Annotation Pyhmmer Darwinomics Proto Gene Annotation Pyhmmer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Mutagenesis Random Nucleotide Darwinomics Proto Mutagenesis Random Nucleotide runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Mutagenesis Random Protein Darwinomics Proto Mutagenesis Random Protein applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable sequence data Darwinomics Proto Orf Prediction Orfipy Darwinomics Proto Orf Prediction Orfipy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Orf Prediction Prodigal Darwinomics Proto Orf Prediction Prodigal runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Sequence Alignment Blast Darwinomics Proto Sequence Alignment Blast handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable sequence data Darwinomics Proto Sequence Alignment Mafft Darwinomics Proto Sequence Alignment Mafft handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable sequence data Darwinomics Proto Sequence Alignment Mmseqs2 Darwinomics Proto Sequence Alignment Mmseqs2 handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable sequence data Darwinomics Proto Sequence Scoring Segmasker Darwinomics Proto Sequence Scoring Segmasker runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequence data Darwinomics Proto Structure Alignment Foldmason Darwinomics Proto Structure Alignment Foldmason handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable protein or structure data Darwinomics Proto Structure Alignment Foldseek Darwinomics Proto Structure Alignment Foldseek handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable protein or structure data Darwinomics Proto Structure Alignment Pymol Rmsd proto structure alignment pymol rmsd Tools Runnable protein or structure data Darwinomics Proto Structure Alignment Tmalign Darwinomics Proto Structure Alignment Tmalign handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable protein or structure data Darwinomics Proto Structure Alignment Usalign Darwinomics Proto Structure Alignment Usalign handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable protein or structure data Darwinomics Proto Structure Prediction Viennarna Darwinomics Proto Structure Prediction Viennarna applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable sequence data Darwinomics Proto Structure Prediction X3dna Darwinomics Proto Structure Prediction X3dna applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data Darwinomics Proto Structure Scoring Dssp Darwinomics Proto Structure Scoring Dssp applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data Darwinomics Proto Structure Scoring Ipsae Darwinomics Proto Structure Scoring Ipsae applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data Darwinomics Proto Structure Scoring Pdockq2 Darwinomics Proto Structure Scoring Pdockq2 applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data Darwinomics Proto Structure Scoring Pyrosetta Darwinomics Proto Structure Scoring Pyrosetta applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable protein or structure data Darwinomics Proto Structure Scoring Structure Metrics proto structure scoring structure metrics Tools Runnable protein or structure data Darwinomics Validation Analysis Execution Runner Execute validation analysis plan and emit run manifest with step results, artifacts, and structured telemetry. Tools Runnable sample metadata Darwinomics Validation Analysis Scope Addendum Deterministic advisory scope addendum for DarwinOmics paper validation reports. Tools Runnable Analysis tool Darwinomics Validation Article Schema Document Builder Build structured research article document from source materials using article schema. Tools Runnable Analysis tool Darwinomics Validation Artifact Evidence Deterministic artifact evidence primitive for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Artifact Lineage Deterministic artifact provenance and paper-output lineage graph for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Certificate Gate Deterministic certificate readiness gate for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Data Acquisition Planner Convert paper scope and source materials into a deterministic data acquisition plan. Tools Runnable Analysis tool Darwinomics Validation Dcrf Bulk Ingest Converter Bulk convert downloaded source data into research data artifact artifacts in parallel. Tools Runnable sample metadata Darwinomics Validation Deterministic Audit Deterministic evidence audit for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Evidence Manifest Deterministic evidence ledger builder for DarwinOmics validation reports. Tools Runnable sample metadata Darwinomics Validation Execution Plan Builder Build validation execution graph from paper targets, derivation requirements, and research data artifact assets. Tools Runnable Analysis tool Darwinomics Validation Grounding Convergence Harness Run iterative KG grounding passes over model prompts and responses until hallucination risk falls below threshold. Tools Runnable Analysis tool Darwinomics Validation Model Review Orchestrator Run multi-model structured review loop and return approval, rejection, or correction packets. Tools Runnable Analysis tool Darwinomics Validation Numeric Target Comparator Compare approved paper-side structured values to reproduced structured outputs with deterministic rules. Tools Runnable Analysis tool Darwinomics Validation Paper De Claims Deterministic paper DE aggregate claim extraction primitive for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Paper Output Comparison Deterministic paper-output comparison mapper for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Paper Output Reconciliation Deterministic paper-output reconciliation for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Paper Reader Target Mapping Deterministic paper-reader target to comparison-row mapping primitive. Tools Runnable Analysis tool Darwinomics Validation Paper Replication Schema Deterministic paper replication schema primitive for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Paper Review Segments Deterministic paper-review segment evidence bundle for schema-driven DarwinOmics validation. Tools Runnable Analysis tool Darwinomics Validation Paper Scope Audit Deterministic paper-scope completeness audit for DarwinOmics paper validation. Tools Runnable Analysis tool Darwinomics Validation Paper Scope Extractor Extract paper analytical scope, data scope, contrasts, endpoints, and claimed outputs from structured article document. Tools Runnable Analysis tool Darwinomics Validation Paper Source Acquirer Resolve and acquire public paper sources, metadata, full text, figures, supplements into a hashable source bundle. Tools Runnable Analysis tool Darwinomics Validation Paper Specific Framework Deterministic paper-specific framework object for DarwinOmics validation gates. Tools Runnable Analysis tool Darwinomics Validation Paper Target Contract Builder Build paper target analysis element mapping declared scope and outputs to reproduction outputs and comparison rules. Tools Runnable Analysis tool Darwinomics Validation Paper Target Review Chain Approve or reject paper target analysis element through reviewer chain and return hash-bound approval artifact. Tools Runnable Analysis tool Darwinomics Validation Primary Json Inspection Deterministic primary JSON evidence completeness gate for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Process Trace Deterministic structured event trace bundle for DarwinOmics validation workflows. Tools Runnable Analysis tool Darwinomics Validation Public Data Downloader Download planned public data assets into run-scoped storage with checksums and manifests. Tools Runnable Analysis tool Darwinomics Validation Public Release Gate Deterministic public-release approval gate for DarwinOmics validation records. Tools Runnable Analysis tool Darwinomics Validation Public Report Surface Deterministic sanitizer for reviewer-facing DarwinOmics validation report JSON. Tools Runnable Analysis tool Darwinomics Validation Replication Findings Deterministic replication findings and audit bundle for DarwinOmics paper validation. Tools Runnable Analysis tool Darwinomics Validation Report Package Builder Assemble public and admin validation report packages from structured evidence and comparisons. Tools Runnable Analysis tool Darwinomics Validation Researcher Derivation Planner Separate researcher-created intermediate assets from public raw data and determine reproduction obligations. Tools Runnable Analysis tool Darwinomics Validation Schema Correction Packet Deterministic correction packet for schema-gate failures in DarwinOmics paper validation. Tools Runnable Analysis tool Darwinomics Validation Schema Gate Deterministic DarwinOmics research article schema completeness gate. Tools Runnable Analysis tool Darwinomics Validation Source Materials Ingest Deterministic DarwinOmics source-material research data artifact normalization for paper validation. Tools Runnable Analysis tool Darwinomics Validation Step Output Evidence Deterministic step-output evidence primitive for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Structured Telemetry Emitter Emit normalized structured status, heartbeat, timing, artifact, and blocker events for validation steps. Tools Runnable protein or structure data Darwinomics Validation Target Review Gate Deterministic target-review approval gate for DarwinOmics validation. Tools Runnable Analysis tool Darwinomics Validation Target Spec Merge Deterministic target-specification correction merge for DarwinOmics paper validation. Tools Runnable Analysis tool Darwinomics Validation Tool Evidence Deterministic tool evidence primitive for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Visual Evidence Index Deterministic public visual evidence index for DarwinOmics paper validation reports. Tools Runnable Analysis tool Darwinomics Validation Visual Reference Pair Builder Build report-time side-by-side visual reference pairs from paper panel snips and DarwinOmics plots. Tools Runnable Analysis tool Darwinomics Validation Visual Reproduction Evidence Deterministic visual reproduction evidence bundle for DarwinOmics validation reports. Tools Runnable Analysis tool Darwinomics Validation Workflow State Controller Control validation stage transitions using structured module outputs, gates, blockers, and resume tokens. Tools Runnable Analysis tool Dcrfsegmentation Normalize Dcrfsegmentation Normalize processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable Analysis tool Deepimagej Deepimagej processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Deeptools Deeptools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Deeptools Bamcoverage Computes coverage depth across the genome from BAM files. Produces bigWig coverage tracks for visualization. Tools Runnable Analysis tool Deeptools Computematrix Computes signal intensity over genomic regions for heatmap visualization. Tools Runnable expression matrices Delly Call structural variants using DELLY. Tools Runnable Analysis tool DESeq2 Research-certified Rust-native DESeq2 1.52.0 fixture executor for research data artifact to research data artifact. Tools Runnable expression matrices thelovelab/DESeq2 | 465 stars DESeq2 Container DESeq2 Container supports differential analysis from expression matrices, preserving effect sizes, test statistics, and result tables for comparison. Tools Runnable expression matrices thelovelab/DESeq2 | 465 stars Diablo Diablo runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Dialignr Dialignr handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable sequencing reads Diapasefmethod Diapasefmethod runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Difftf Difftf runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Doubletfinder Doubletfinder runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Drop Drop runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Dynverse Dynverse runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Eager2 Eager2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Eagle Rc Eagle Rc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Eagle2 Eagle2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Easypqp Easypqp runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Edger Research-certified Rust-native edgeR GLM quasi-likelihood fixture executor for research data artifact to research data artifact. Tools Runnable expression matrices Edta Edta runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Effectsize R Effectsize R runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ehdn Ehdn runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Embedding Cluster Embedding Cluster renders dimensionality-reduction views from matrices or embeddings for clustering, separation, and quality-control review. Tools Runnable Analysis tool Embedding Similarity Embedding Similarity renders dimensionality-reduction views from matrices or embeddings for clustering, separation, and quality-control review. Tools Runnable Analysis tool Encyclopedia Encyclopedia runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Enigma Protocols Enigma Protocols runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Enrichr Enrichr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Enrichr Client Enrichr Client runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ensembl Vep Ensembl Vep supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Tools Runnable variant calls Epiage Epiage runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Epic Epic runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Episcanpy Episcanpy supports single-cell analysis, annotation, or embedding workflows with reproducible matrix and metadata handling. Tools Runnable sequencing reads scverse/scanpy | 2,497 stars Exomiser Cli Exomiser Cli runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Exomiser Clinical Exomiser Clinical runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Expansionhunter Expansionhunter runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Fabric Genomics Fabric Genomics runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Facets Facets runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Farmcpu Farmcpu runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Fastp Research-certified Rust-native fastp 1.3.4-compatible single-end cut_front/cut_tail Q20 trimming for research data artifact. Tools Runnable sequencing reads OpenGene/fastp | 2,384 stars FastQC Analyzes sequencing read quality and produces a comprehensive quality report. Checks per-base sequence quality, per-sequence quality scores, sequence duplication levels, adapter contamination, GC content distribution, and overrepresented... Tools Runnable sequencing reads s-andrews/FastQC | 602 stars Faststructure Faststructure applies protein, sequence, or structure modeling as a traceable analysis step with captured inputs and generated outputs. Tools Runnable Analysis tool Fateid Fateid runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Featurecounts featureCounts counts reads mapping to genomic features. Standard tool for RNA-seq quantification. Fast, accurate, supports strand-specific counting. Tools Runnable Analysis tool Fgsea Fast gene set enrichment analysis using fgsea. Tools Runnable Analysis tool FHIR Tools FHIR Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Figtree Figtree runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Finemap Fm Finemap Fm runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Fish Quant Fish Quant quantifies reads, transcripts, or feature counts so expression-level results can be regenerated and compared. Tools Runnable image or spatial data Flair Flair runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Flair Lr Flair Lr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Flashlfq Flashlfq runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Flashweave Flashweave runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Flye Assemble long reads using Flye. Tools Runnable Analysis tool Fpocket Fpocket runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Franklin Franklin runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Fraser Fraser runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Fraser2 Fraser2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Freebayes Call variants using Bayesian haplotype-based method. Tools Runnable Analysis tool Fsl Freesurfer Fsl Freesurfer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Fusion Fs Fusion Fs runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool G Power G Power runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Galaxy Platform Galaxy Platform runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gapit Gapit runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool GATK Base Recalibrator GATK Base Quality Score Recalibration (BQSR). Adjusts base quality scores using known variant sites. Part of GATK Best Practices for germline variant calling. Tools Runnable aligned sequencing reads broadinstitute/gatk | 1,970 stars GATK Mutect2 GATK Mutect2 calls somatic SNPs and indels from tumor-normal or tumor-only data. Standard for cancer variant calling. Tools Runnable aligned sequencing reads broadinstitute/gatk | 1,970 stars GATK4 GATK4 supports variant calling, normalization, or annotation so genomic findings can be reproduced from the supplied evidence. Tools Runnable Analysis tool broadinstitute/gatk | 1,970 stars Gcta Gcta runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Genomic Prediction Genomic Prediction runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Genotify Genotify runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Giotto Giotto runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gisaid Cli Gisaid Cli runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Glimma Glimma supports differential analysis from expression matrices, preserving effect sizes, test statistics, and result tables for comparison. Tools Runnable expression matrices Glmmtmb Glmmtmb runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gmx Mmpbsa Gmx Mmpbsa runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gnps Gnps runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gpower Gpower runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gprofiler Gprofiler runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gridss Gridss runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gromacs Gromacs handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads Gsdesign Gsdesign runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gseapy Gseapy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gspower Gspower runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gubbins Gubbins runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Gwaspoly Gwaspoly runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Hapne Hapne runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Harmony Integrate single-cell datasets using Harmony. Tools Runnable Analysis tool Helical Helical runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Hiccups Hiccups runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Hifiasm Assemble PacBio HiFi reads using hifiasm. Tools Runnable Analysis tool Hisat2 Memory-efficient splice-aware alignment with HISAT2. Tools Runnable sequencing reads DaehwanKimLab/hisat2 | 539 stars Hisat2 Align HISAT2 aligns RNA-seq reads using a hierarchical index. Uses ~8GB RAM vs 32GB for STAR. Use HISAT2 when memory is limited or as an alternative to STAR. Tools Runnable sequencing reads DaehwanKimLab/hisat2 | 539 stars HL7 FHIR Tools HL7 FHIR Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Homer Homer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Horvath Clock Horvath Clock runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool HPO Toolkit HPO Toolkit runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Igv Desktop Igv Desktop runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool igvteam/igv.js | 725 stars Immunedeconv Immunedeconv runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Inspiired Inspiired runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Instrain Instrain runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Interpro Interpro runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Interproscan Interproscan runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Intervar Intervar runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Isoquant Isoquant handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads Ivar Ivar runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Jasmine Jasmine runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Junction Quantify Junction Quantify turns tabular analysis results into report-ready plots that can be checked against the figures in a submitted study. Tools Runnable aligned sequencing reads Kallisto Quantify transcript expression using Kallisto pseudo-alignment. Tools Runnable aligned sequencing reads Kallisto Bustools Kallisto Bustools handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads Kbet Kbet runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Kraken2 Classify reads taxonomically using Kraken2. Tools Runnable sequencing reads Kraken2 Classify Kraken2 classifies metagenomic sequence reads using k-mer matching. Identifies organisms present in mixed microbial samples. Tools Runnable sequencing reads Ksea App Ksea App runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Larry Larry runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Lazyslide Lazyslide processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Ldhub Ldhub runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ldpred2 Ldpred2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ldsc Ldsc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Lefse Lefse runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Leiden Leiden clustering identifies cell populations in single-cell data using community detection on a KNN graph. Produces more well-defined clusters than Louvain. Use after UMAP to identify cell types. Tools Runnable Analysis tool Lifelines Lifelines runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Liftoff Liftoff runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Limma Research-certified Rust-native limma/edgeR voom fixture executor for research data artifact to research data artifact. Tools Runnable expression matrices Lims Connector Lims Connector runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Lipidcreator Lipidcreator runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Lipidsearch Lipidsearch runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Lme4 Lme4 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Lofreq Lofreq runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Loinc Mapper Loinc Mapper runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Maaslin2 Maaslin2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Macs2 Call peaks from ChIP-seq/ATAC-seq data using MACS2. Tools Runnable aligned sequencing reads Macs2 Callpeak MACS2 identifies protein-DNA interaction sites from ChIP-seq or ATAC-seq data. Models fragment length and uses dynamic Poisson distribution for peak detection. Always provide a control sample when available. Tools Runnable aligned sequencing reads Macs3 Call peaks using MACS3 (next generation MACS). Tools Runnable aligned sequencing reads Mageck Mageck supports microbiome or metagenomic analysis so taxonomic, assembly, or quality results can be regenerated. Tools Runnable Analysis tool Manta Call structural variants using Manta. Tools Runnable Analysis tool Marugoto Marugoto processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Mash Mash runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mast Mast runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Matchms Matchms runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mcmicro Mcmicro runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mcp Counter Mcp Counter runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mcscanx Mcscanx runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mediation Mediation runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Meme Suite Meme Suite runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mendelian Randomization Mendelian Randomization runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Merip Tools Merip Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Merqury Merqury runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Metafor Metafor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Metafor R Metafor R runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Metal Metal runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Methyldackel Methyldackel handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads Mice Imputation Mice Imputation runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Microreact Microreact runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Midas2 Tool Midas2 Tool runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Minigraph Minigraph runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Minigraph Pg Minigraph Pg runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Minimac4 Minimac4 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Minimap2 Align long reads (Nanopore/PacBio) using minimap2. Tools Runnable sequencing reads Minimap2 Align Minimap2 aligns long reads (PacBio, Oxford Nanopore) to a reference genome. Optimized for long, noisy reads. For short Illumina reads, BWA-MEM is generally more accurate. Tools Runnable sequencing reads Missforest Missforest runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mixcr Mixcr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mixomics R Mixomics R runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mixomics V2 Mixomics V2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mmvec Mmvec runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Modkit Modkit runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Modkit Nano Modkit Nano runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool MOFA Plus MOFA Plus runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mokapot Mokapot runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Molin Molin runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Monocle3 Traj Monocle3 Traj runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mothur Mothur runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Mrtrix3 Mrtrix3 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Ms Dial Ms Dial runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Msa Search NIM Msa Search NIM handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable sequence data NVIDIA-BioNeMo/bionemo-recipes | 806 stars Msbuddy Msbuddy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Msconvert Msconvert runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Msdial Msdial runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Msdial Tool Msdial Tool runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Msstats Msstats runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Msstats Tool Msstats Tool runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Multiqc Aggregates quality metrics from multiple FastQC runs into a single comprehensive report. Use when you have QC metrics from multiple samples and want to compare them side by side. Tools Runnable Analysis tool MultiQC/MultiQC | 1,466 stars Mummichog Mummichog runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Muon Muon runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Muscat Muscat runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Catalog Analysis tool Mutect2 Call somatic variants from tumor-normal pairs using Mutect2. Tools Runnable aligned sequencing reads Nano Esm2 Embedding Nano Esm2 Embedding renders dimensionality-reduction views from matrices or embeddings for clustering, separation, and quality-control review. Tools Runnable Analysis tool facebookresearch/esm | 4,140 stars Nano RNA-seq Nano RNA-seq runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Nano Samtools Sort Nano Samtools Sort handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads samtools/samtools | 1,918 stars Nanofilt Rust-native NanoFilt 2.8-compatible long-read filtering for research data artifact. Tools Runnable sequencing reads Nanostat Nanostat runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sequencing reads Napari Napari runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Napari Plugin Runner Napari Plugin Runner processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Neuromaps Neuromaps runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Nextflow Runner Nextflow Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sample metadata nextflow-io/nextflow | 3,426 stars Nextstrain Nextstrain runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Nf Schema Nf Schema runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Nf Test Nf Test runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Omicade4 Omicade4 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Oncokb Annotator Oncokb Annotator runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Openmm Md Openmm Md runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Openms Openms runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Openswath Openswath runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Optitype Optitype runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Outrider Outrider runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Paintor Paintor runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Palantir Palantir runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Paste Spatial Paste Spatial processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable Analysis tool Patch seq Tools Patch seq Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pathogenwatch Pathogenwatch runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pbmm2 Pbmm2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Perseus Perseus runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pharmvar API Pharmvar API runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Phaster Phaster runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Phenix Phenix runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Phenopackets Phenopackets runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Phenopackets Tools Phenopackets Tools runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Phosr Phosr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Phyloseq Phyloseq runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Picard Mark duplicates, sort, and manipulate BAM files using Picard. Tools Runnable Analysis tool Planemo Planemo runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sample metadata Plasmidfinder Plasmidfinder runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pointfinder Pointfinder runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Progeny Progeny runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Prokka Annotate bacterial genomes using Prokka. Tools Runnable Analysis tool Proteome Discoverer Proteome Discoverer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Proteowizard Proteowizard runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Prs Cs Prs Cs runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Prsice2 Prsice2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Psmc Psmc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Purple Purple runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pwr Pwr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pwr R Pwr R runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pydeseq2 Pydeseq2 supports differential analysis from expression matrices, preserving effect sizes, test statistics, and result tables for comparison. Tools Runnable expression matrices thelovelab/DESeq2 | 465 stars Pymc Pymc runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pyopenms Pyopenms runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pypgx V2 Pypgx V2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Pyteomics Pyteomics runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Qiime2 Qiime2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Quast Quast runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Qupath Qupath processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Ragtag Ragtag runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Raxml Ng Raxml Ng runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rctd Rctd runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Recon3d Recon3d runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Relion Relion runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Repeatmodeler2 Repeatmodeler2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Reportlab Genomics Reportlab Genomics runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Resfinderfg Resfinderfg runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rfmix2 Rfmix2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rose Enhancer Rose Enhancer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rosetta Suite Rosetta Suite runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rpact Rpact runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rrblup Rrblup runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Rs Fish Rs Fish processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable image or spatial data Rsem Rsem runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sage Sage runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sage Proteomics Sage Proteomics runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Saint Express Saint Express handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads Salmon Quantify transcript expression using Salmon quasi-mapping. Tools Runnable aligned sequencing reads COMBINE-lab/salmon | 901 stars Salmon Quant Salmon quantifies transcript-level expression using quasi-mapping. Faster than alignment-based methods. Can also quantify from aligned BAM files. Tools Runnable aligned sequencing reads COMBINE-lab/salmon | 901 stars Samplesizer Samplesizer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Samplesizr Samplesizr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Samtools View, sort, index, and manipulate BAM/SAM alignment files. Tools Runnable Analysis tool samtools/samtools | 1,918 stars Samtools Index Creates BAM index (.bai) file required for random access and visualization. Tools Runnable Analysis tool samtools/samtools | 1,918 stars Samtools Markdup Marks duplicate reads in coordinate-sorted BAM. Required before variant calling to reduce PCR artifacts. Tools Runnable aligned sequencing reads samtools/samtools | 1,918 stars Samtools Sort Sorts BAM/SAM alignments by coordinate. Required before indexing and downstream analysis. Tools Runnable aligned sequencing reads samtools/samtools | 1,918 stars Scanorama Batch-correct single-cell data using Scanorama. Tools Runnable Analysis tool Scanpy Preprocess, cluster, and embed single-cell data using Scanpy. Tools Runnable sequencing reads scverse/scanpy | 2,497 stars Scanpy Preprocess Standard single-cell RNA-seq preprocessing: filter cells by gene count, filter genes by cell count, normalize, log transform, identify highly variable genes. Essential first step before UMAP and clustering. Tools Runnable sequencing reads scverse/scanpy | 2,497 stars Scib Scib runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Scirpy Scirpy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Scope2 Scope2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Scrublet Scrublet runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Scverse Ecosystem Scverse Ecosystem runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Segmentation Count Segmentation Count processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable Analysis tool Segmentation Quantify Segmentation Quantify quantifies reads, transcripts, or feature counts so expression-level results can be regenerated and compared. Tools Runnable Analysis tool Segmentation To Singlecell Converts spatial segmentation masks into a single-cell expression matrix. Maps segmentation regions to gene expression spots. Tools Runnable sequencing reads Selscan Selscan runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Seqera Cli Seqera Cli runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Seqera Platform Seqera Platform runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Seqr Seqr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sequence Validate Validates DNA, RNA, and protein sequence rows and emits explicit per-row research data artifact validation reports. Tools Runnable sequence data Sequenza Sequenza runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Seurat Analyze single-cell data using Seurat R package. Tools Runnable Analysis tool satijalab/seurat | 2,759 stars Seurat Spatial Seurat Spatial supports single-cell analysis, annotation, or embedding workflows with reproducible matrix and metadata handling. Tools Runnable Analysis tool satijalab/seurat | 2,759 stars Shapeit4 Shapeit4 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Signac Signac runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool satijalab/seurat | 2,759 stars Simr Simr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Singler Singler runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Skat Skat runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Skyline Daily Skyline Daily runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Skyline Tool Skyline Tool runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sleuth Sleuth runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Slingshot Slingshot runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Smoove Smoove runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Snakemake Runner Snakemake Runner runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable sample metadata snakemake/snakemake | 2,820 stars Snapatac2 Snapatac2 handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable aligned sequencing reads Snomed Mapper Snomed Mapper runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Snpeff Annotate variants with functional effects using SnpEff. Tools Runnable variant calls Sodb Client Sodb Client runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Songbird Songbird runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Soupx Soupx runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sourmash Sourmash runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Spacemake Spacemake runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Spades De novo genome assembly using SPAdes. Tools Runnable sequencing reads Spatialdata Spatialdata processes image or spatial data into reviewable analysis artifacts while preserving file and metadata provenance. Tools Runnable Analysis tool Spectronaut Spectronaut runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Spieceasi Spieceasi runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sqanti3 Sqanti3 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Sragent Sragent runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Star Splice-aware RNA-seq alignment using STAR. Tools Runnable Analysis tool Star Align STAR (Spliced Transcripts Alignment to a Reference) aligns RNA-seq reads to a reference genome. Best for long RNA-seq reads. Requires 32GB RAM for human genome. Use HISAT2 for memory-constrained environments. Tools Runnable sequencing reads alexdobin/STAR | 2,216 stars Stargazer2 Stargazer2 handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable Analysis tool Starsolo Starsolo handles read alignment or aligned-read processing with captured inputs, parameters, and output artifacts for reproducibility review. Tools Runnable Analysis tool alexdobin/STAR | 2,216 stars Steinbock Steinbock runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Stellarpgx Stellarpgx runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Stemnet Stemnet runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Stereopy Stereopy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Stlearn Stlearn runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Stlearn St Stlearn St runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Strainphlan Strainphlan runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Strelka2 Call somatic small variants using a deterministic local pileup caller. Tools Runnable aligned sequencing reads Stripy Stripy runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Survival R Survival R runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Survminer Survminer runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Susie Fm Susie Fm runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Svaba Svaba runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Synvisio Synvisio runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Tabix Tabix runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Tassel5 Tassel5 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Thermorawfileparser Thermorawfileparser runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Tobias Tf Tobias Tf runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Transmission Tree Transmission Tree runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Transphylo Transphylo runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Treetime Treetime runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Trim Galore Removes adapter sequences and low-quality bases from sequencing reads. Automatically detects Illumina Universal, Nextera, and Small RNA adapters. Removes low-quality bases from read ends and discards reads shorter than minimum length. Tools Runnable sequencing reads FelixKrueger/TrimGalore | 561 stars Trimmomatic Research-certified Rust-native Trimmomatic 0.40-compatible single-end SLIDINGWINDOW:4:20 trimming for research data artifact. Tools Runnable sequencing reads Trinity Trinity runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Tutorial Sandbox Tutorial Sandbox runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Twosamplemr Twosamplemr runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Varsome Varsome runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool VCF Filter Filters VCF variants by quality, depth, allele frequency, and other criteria. Removes low-quality variant calls. Use after variant calling to clean up results. Tools Runnable sequencing reads VCF Normalize Normalizes VCF variants: left-aligns indels, splits multiallelic sites. Required before variant annotation and downstream analysis. Tools Runnable aligned sequencing reads Vep Annotate variants using Ensembl VEP. Tools Runnable variant calls Virsorter2 Virsorter2 runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Vitessce Tool Vitessce Tool runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Wave Cli Wave Cli runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Wot Wot runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool Xcms Online Xcms Online runs a traceable analysis step with captured inputs, parameters, outputs, and provenance for paper-replication review. Tools Runnable Analysis tool