Browse Tools

UCSF ChimeraX — next-generation molecular visualization and analysis tool for structural biology. Provides interactive 3D visualization of proteins, nucleic acids, cryo-EM density maps, and molecular

Use when working with chipseeker — chIPseeker — R/Bioconductor package

ClinVar submission tools — NCBI REST API client and Python utilities for submitting variant pathogenicity interpretations to NCBI ClinVar. Supports germline and somatic variant classifications, oncoge

ClonalFrameML detects recombination (horizontal gene transfer) in bacterial whole-genome alignments using maximum likelihood inference. It takes a Newick phylogenetic tree and FASTA/XMFA alignment, th

clusterProfiler — universal enrichment analysis tool for interpreting omics data using Gene Ontology, KEGG pathways, WikiPathways, Reactome, Disease Ontology, and custom gene sets. Implements over-rep

cmprsk — Subdistribution Analysis of Competing Risks. R package providing non-parametric cumulative incidence estimation via cuminc() with Gray's K-sample test for group comparisons, Fine & Gray propo

Cobolt — Bayesian multi-modal variational autoencoder for joint analysis of single-cell multi-omics data, especially paired snRNA-seq and snATAC-seq. Learns a shared latent representation across gene

COLOC (coloc) -- R package for Bayesian colocalization analysis of genetic associations. Tests whether two traits share a causal variant at a genomic locus using GWAS summary statistics. Implements co

Colony is a maximum-likelihood program for sibship reconstruction and parentage assignment from genetic marker data (microsatellites, SNPs, AFLPs). Developed at the Zoological Society of London (ZSL),

ComplexHeatmap — R/Bioconductor package for creating highly customizable heatmaps with complex annotations. Supports row/column splitting, multiple annotation tracks (bar, box, point, histogram), Onco

cooltools — Python toolkit for Hi-C and chromosome conformation capture analysis in the Open2C ecosystem. Analyzes .cool format contact maps to compute A/B compartments (eigenvectors), insulation scor

CopyKAT (Copy number Karyotyping of Tumors) — R package for inferring genome-wide aneuploidy and copy number variations from single-cell RNA-seq data. Uses Bayesian segmentation to distinguish tumor (

CRISPR-DAV (CRISPR DNA Analysis and Visualization) is a pipeline for analyzing and visualizing CRISPR editing outcomes from amplicon sequencing (NGS) data. Detects indels, substitutions, HDR events, a

Use when working with CRISPRcleanR — an R package for unsupervised correction of copy-number-driven biases and off-target effects in CRISPR pooled knock-out screens. Normalizes sgRNA read counts, remo

Cromwell/WDL — Broad Institute workflow execution engine and WDL (Workflow Description Language) for defining, running, and scaling bioinformatics pipelines. Cromwell executes WDL workflows locally, o

Cumulus — cloud-based framework for large-scale single-cell and single-nucleus RNA-seq analysis on Terra/Google Cloud. Provides WDL workflows for demultiplexing (demuxEM, souporcell, demuxlet), count

Use when visualizing, analyzing, or manipulating biological networks with Cytoscape, the industry-standard desktop platform for systems biology and pathway analysis. Covers network import (SIF, XGMML,

CytoTRACE -- computational method for predicting relative differentiation state of cells from single-cell RNA-seq data. Uses gene counts (number of detectably expressed genes per cell) as a robust pro

Dash Bio -- interactive bioinformatics visualization components built on Plotly Dash. Provides domain-specific charts including Circos plots, ideograms, needle plots (lollipop/mutation diagrams), alig

Use when working with dbCAN — run_dbcan — for CAZyme annotation of protein or genome sequences from metagenomics and microbiome studies. Annotates Carbohydrate-Active enZymes (CAZymes) including glyco

DBSCAN (Density-Based Spatial Clustering of Applications with Noise) — fast C++ implementation of density-based clustering algorithms in R. Includes DBSCAN, HDBSCAN, OPTICS/OPTICSXi, LOF outlier detec

DECIPHER (DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources) — Wellcome Sanger Institute web platform for interpreting pathogenic copy number variants (CNVs), chromosom

deconstructSigs — R package for decomposing tumor somatic mutation patterns into known mutational signature contributions. Converts SNV calls to a 96-trinucleotide context matrix, then applies constra

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

Decoupler -- Python framework for inferring biological activities from omics data. Estimates transcription factor (TF) activities, pathway activities, and ligand-receptor interactions from gene expres

DeepCell — deep learning library for single-cell analysis of biological images using TensorFlow. Provides pretrained models for cell segmentation including Mesmer (multiplexed tissue imaging), nuclear

Use when working with destiny — an R/Bioconductor package for diffusion maps and pseudotime analysis of single-cell RNA-seq data. Computes diffusion components to visualise and order cells along diffe

DEXSeq -- R/Bioconductor package for testing differential exon usage (DEU) from RNA-seq data. Uses a generalized linear model framework (negative binomial distribution) to detect exons whose relative

Use when working with Dfam — the database of repetitive DNA families

DIA-NN (Data-Independent Acquisition by Neural Networks) is a universal software suite for DIA proteomics data analysis. Processes raw mass spectrometry files (.mzML, .raw, .d, .wiff) using neural net

DIA-NN R package — R toolkit for post-processing DIA-NN proteomics search results. Provides report loading (diann_load), precursor/peptide/protein matrix generation with FDR filtering (diann_matrix),

DiffBind — Bioconductor R package for differential binding analysis of ChIP-seq and ATAC-seq data. Computes read count overlaps from BAM files at consensus peak sets, normalizes with DESeq2 or edgeR,

Use when working with Dipy — the Python library for diffusion MRI analysis. Covers diffusion tensor imaging (DTI), constrained spherical deconvolution (CSD), diffusion kurtosis imaging (DKI), IVIM, fi

dmrseq is an R/Bioconductor package for detecting differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) data. It fits a generalized least squares model with a smooth c

DRAGEN (Dynamic Read Analysis for GENomics) — Illumina's FPGA-accelerated bioinformatics platform for secondary analysis of next-generation sequencing data. Performs hardware-accelerated mapping, alig

Use when working with EmptyDrops or DropletUtils — the Bioconductor R package for distinguishing real cells from empty droplets in droplet-based single-cell RNA-seq data (10x Genomics, Drop-seq, inDro

ENCODE ChIP-seq pipeline — official ENCODE DCC WDL/Cromwell pipeline for transcription factor (TF) and histone mark ChIP-seq analysis. Handles adapter trimming (Trimmomatic), alignment (Bowtie2/BWA),

ENmix — R/Bioconductor package for quality control, background correction, and normalization of Illumina DNA methylation array data (EPIC, 450K, EPIC v2). Provides ENmix background correction, RELIC d

ESMFold — end-to-end single-sequence protein structure prediction using the ESM-2 protein language model. Predicts 3D atomic coordinates directly from amino acid sequence without multiple sequence ali

ETE Toolkit — Python library for phylogenetic tree exploration, manipulation, and analysis. Provides tree parsing (Newick, Nexus), database connectivity (NCBI Taxonomy, GTDB), interactive visualizatio

Exomiser -- Java application for phenotype-driven variant prioritization in rare disease diagnosis. Filters and ranks variants from VCF files using Human Phenotype Ontology (HPO) terms, cross-species

fastools — A Python-based toolkit by Jeroen F.J. Laros for the manipulation and characterization of FASTA and FASTQ files. Use when performing sequence conversions, filtering by length, generating seq

fgsea — fast preranked gene set enrichment analysis in R using an adaptive multi-level split Monte-Carlo scheme for arbitrarily precise GSEA p-values. Provides fgsea(), fgseaMultilevel(), plotEnrichme

FigTree — interactive Java-based phylogenetic tree viewer for displaying, annotating, and exporting phylogenetic trees produced by BEAST, BEAST2, MrBayes, RAxML, IQ-TREE, or any NEXUS/Newick tree file

FINEMAP — Bayesian fine-mapping tool for identifying causal variants from GWAS summary statistics and linkage disequilibrium (LD) matrices. Uses shotgun stochastic search to enumerate causal configura

flashfm — Bayesian multi-trait fine-mapping of GWAS summary statistics using the JAM (Joint Analysis of Marginal statistics) framework. Identifies shared and trait-specific causal variants across mult

Foldseek — fast protein structure search and clustering using the 3Di structural alphabet. Compares protein structures at sequence-search speed, supporting monomer and multimer searches, structural cl

folium — interactive geospatial maps in Python. Create choropleth maps, marker clusters, heatmaps, and tile-layer maps using folium.Map(), add GeoJSON overlays with folium.GeoJson() and folium.Choropl

Tools for working with categorical variables (factors) in R. Includes functions for reordering levels (fct_reorder, fct_infreq, fct_relevel), modifying level values (fct_recode, fct_lump, fct_collapse

fqtools — fast FASTQ file manipulation suite written in C. Provides 16 subcommands for viewing, filtering, trimming, converting, and validating FASTQ files. Supports gzip-compressed and BAM input nati