Browse Tools

Differential expression analysis of RNA-seq and other count data using empirical Bayes estimation of the dispersion parameter for the negative binomial model.

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ConsensusClusterPlus — R/Bioconductor package for determining cluster count and membership by stability evidence in unsupervised analysis, implementing the Monti et al. (2003) consensus clustering alg

iClusterPlus — Bioconductor R package for integrative clustering of multi-omics data. Performs joint latent variable modeling of multiple genomic data types (e.g., SNP copy number, methylation, gene e

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

MAFFT — multiple sequence alignment for nucleotide and protein sequences. Implements progressive (FFT-NS-1, FFT-NS-2), iterative refinement (FFT-NS-i), and consistency-based iterative methods (L-INS-i

DoE.base is a foundational R package by Ulrike Groemping for full factorial experimental designs and designs based on orthogonal arrays. It provides utility functions for the shared `design` class use

Query STRING API for protein-protein interaction networks, functional enrichment, and interaction partner discovery. Covers 59M proteins across 5000+ species with 20B+ scored interactions from 7 evide

GRITS Toolbox is a free, open-source desktop application for processing, annotating, and archiving glycomics mass spectrometry data. It automates MS/MS spectral annotation of glycan fragments against

Programmatic access to the U.S. EPA ToxCast and Tox21 high-throughput screening (HTS) bioactivity data via the CTX APIs. Use to query chemical hazard profiles, AC50 values, and hit-calls across thousa

estimate-compute-requirements — predict CPU, memory, wall time, and storage for bioinformatics pipelines given input data size and tool selection. Generates per-step resource tables, platform-specific

Look up documentation and code examples for bioinformatics tools using BioContext7

Use when converting Illumina BCL (Binary Base Call) files to FASTQ format, demultiplexing sequencing runs by index sequences, or trimming adapters from short-read data. Handles HiSeq, MiSeq, NextSeq,

Use when working with datamash — datamash — GNU command-line tool for

featureCounts — ultrafast read counting program for assigning aligned reads (SAM/BAM) to genomic features such as genes, exons, promoters, and genomic bins. Part of the Subread package. Supports singl

LAST — adaptive-seed sequence aligner for genomes, long reads, and proteins. Uses lastdb to build databases, last-train to learn substitution/gap rates, lastal for alignment, last-split for rearrangem

locfdr — Efron's empirical Bayes local false discovery rate estimation from z-score vectors. Computes per-test posterior probability of being null using a mixture model approach that fits the empirica

NCBI Genome Workbench — desktop application for integrated genomic data visualization, sequence analysis, and annotation. Supports interactive browsing of GenBank/RefSeq entries, multiple sequence ali

Novoalign — high-accuracy short-read sequence aligner for Illumina and MGI platforms using full Needleman-Wunsch algorithm with affine gap penalties. Maps single-end and paired-end reads up to 950bp o

Novocraft suite — short-read alignment and BAM sorting for DNA-seq and RNA-seq. novoalign maps Illumina, Ion Torrent, and 454 reads to indexed reference genomes with Smith-Waterman scoring for high-ac

UNITE is the reference database and taxonomy system for fungal ITS (Internal Transcribed Spacer) metabarcoding and amplicon sequencing. Use for classifying fungal sequences against Species Hypotheses

USEARCH — ultra-fast amplicon sequence analysis toolkit for 16S/ITS/18S microbiome studies. Supports FASTQ quality filtering (fastq_filter), paired-end merging (fastq_mergepairs), dereplication (derep

fetchChromSizes — UCSC Kent utility for retrieving chromosome size tables (chrom.sizes) for any UCSC genome assembly (hg38, hg19, mm10, mm39, dm6, danRer11, sacCer3, etc.). Queries UCSC MySQL or DAS s

GiardiaDB — VEuPathDB genomic resource for the intestinal parasite Giardia lamblia (G. intestinalis, G. duodenalis). Provides gene search, BLAST, genome browsing, functional annotation, ortholog queri

BioGRID — curated repository of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications from the published literature. Provides REST API (v4+) f

BOLT-LMM — efficient linear mixed model association testing for biobank-scale GWAS. Implements infinitesimal and non-infinitesimal Bayesian mixed models with O(MN^1.5) complexity for genome-wide assoc

Cell Ranger ATAC — 10x Genomics official pipeline for processing single-cell ATAC-seq (scATAC-seq) data from raw FASTQ files to peak-barcode matrices and fragment files. Performs barcode demultiplexin

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

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),

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

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

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

KEGG Tools — Kyoto Encyclopedia of Genes and Genomes database access suite for pathway enrichment analysis, gene functional annotation via KEGG Orthology (KO), metabolic pathway reconstruction, and dr

liftOver — UCSC genome coordinate conversion tool for remapping genomic intervals between genome assemblies (e.g., hg19 to hg38, mm10 to mm39). Converts BED, GFF, GTF, VCF, and positional data across

limma-voom — linear models for differential expression analysis of RNA-seq and microarray data. The voom transformation converts RNA-seq read counts to log-CPM with precision weights derived from the

MaizeGDB (Maize Genetics and Genomics Database) — the community database for maize (Zea mays) genetics and genomics. Query gene models, loci, QTLs, traits, germplasm, and metabolites via the MaizeGDB

MEGA (Molecular Evolutionary Genetics Analysis) — cross-platform software suite for phylogenetic tree construction, multiple sequence alignment, molecular evolution analysis, and molecular dating. Sup

MGI/GXD (Mouse Genome Informatics / Gene Expression Database) — authoritative resource for mouse genetics, genomics, and gene expression data maintained by The Jackson Laboratory. Provides comprehensi

OMIM API — programmatic access to the Online Mendelian Inheritance in Man database of human genes and genetic phenotypes. Supports entry lookup by MIM number, full-text search, gene map queries, clini

PanglaoDB — curated single-cell RNA sequencing database providing cell type marker genes, scRNA-seq datasets, and programmatic access tools for cell type annotation. Covers 1,000+ cell types across hu

PharmGKB — Pharmacogenomics Knowledge Base for curated gene-drug relationships, clinical pharmacogenomics annotations, drug pathway diagrams, and VIP gene summaries. Query the PharmGKB REST API for va

Use when querying, downloading, or analysing QTL data from the QTLbase database — a comprehensive multi-tissue, multi-omics QTL repository covering eQTL, sQTL, and pQTL studies across human and model

Roadmap Epigenomics — NIH Roadmap Epigenomics Mapping Consortium reference epigenomes spanning 111 primary human tissues and cell types. Provides ChIP-seq histone mark tracks (H3K4me1, H3K4me3, H3K27m

snpStats is an R/Bioconductor package for GWAS (genome-wide association study) and population genetics analysis. It provides SnpMatrix and XSnpMatrix objects for efficient SNP data storage, PLINK bina

Spectronaut -- commercial DIA (Data-Independent Acquisition) proteomics software from Biognosys for analyzing DIA-MS data. Supports library-based and library-free (directDIA / Pulsar) peptide-centric

Use when working with TxDb.Hsapiens.UCSC.hg38.knownGene, the Bioconductor annotation package providing UCSC hg38 transcript/gene coordinates for Homo sapiens. Handles transcript extraction, exon group

UCSC (University of California Santa Cruz) Bioinformatics — comprehensive routing for all UCSC genomic tools and resources. Covers the UCSC Genome Browser, Table Browser, UCSC MySQL public database, G

Wm82-tools covers bioinformatics workflows for the Glycine max (soybean) Williams 82 (Wm82) reference genome — the primary reference for soybean genomics. Use cases: downloading and indexing Wm82 geno

Use when detecting allele-specific expression (ASE) from RNA-seq data with MBASED, a Bioconductor R package using a meta-analysis-based beta-binomial model. Covers SNP-level and gene-level ASE, phased

ClinVar Database — NCBI's public archive of human genetic variant clinical significance. Query via E-utilities REST API (esearch, esummary, efetch, elink) or download bulk data from FTP in XML, VCF, a