Browse Tools

SuSiE (Sum of Single Effects) — R package for Bayesian variable selection and fine-mapping of GWAS loci. Fits a sparse regression model to identify credible sets of likely causal variants with posteri

sva — R/Bioconductor package for surrogate variable analysis, batch effect correction, and unwanted variation removal in high-throughput experiments. Provides sva() for estimating surrogate variables,

TALON — technology-agnostic long-read transcriptome analysis for identifying and quantifying known and novel genes/isoforms. Works with PacBio and Oxford Nanopore SAM files via a SQLite database backe

totalVI — deep generative model for joint analysis of CITE-seq RNA and surface protein data built on scvi-tools and PyTorch. Provides integrated dimensionality reduction across transcriptome and prote

totalVI and MultiVI — deep generative models from scvi-tools for multi-modal single-cell integration. totalVI jointly models scRNA-seq and protein (CITE-seq) data via a variational autoencoder for den

TransDecoder — identifies candidate coding regions within transcript sequences from de novo RNA-Seq assemblies. Provides TransDecoder.LongOrfs for extracting long open reading frames and TransDecoder.

Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch

Trinotate — comprehensive functional annotation suite for transcriptome assemblies. Integrates BLAST/DIAMOND homology searches against SwissProt, HMMER/Pfam protein domain identification, SignalP sign

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

tximeta — R/Bioconductor package for importing transcript-level quantification data from Salmon, alevin, piscem, and other quantifiers with automatic metadata attachment. Automatically identifies the

tximport -- R/Bioconductor package for importing transcript-level abundance, estimated counts, and transcript lengths from quantification tools (Salmon, Kallisto, RSEM, StringTie, Sailfish) and summar

UCE (Universal Cell Embeddings) — species-agnostic cell embedding model from Stanford SNAP Lab that uses protein language models (ESM-2) to create universal cell representations without species-specif

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

Use when working with VAMB — Variational Autoencoders for Metagenomic Binning — a deep learning tool that groups assembled metagenomic contigs into metagenome-assembled genomes (MAGs). Takes concatena

Use when working with varsome — varSome — comprehensive human genomics

VIBRANT — metagenomics tool for identifying and annotating viruses from microbial assemblies (metagenomes, isolates, and virome datasets). Uses neural networks and KEGG/Pfam/VOG HMM profiles to classi

Vireo (vireoSNP) is a Bayesian variational inference tool for donor demultiplexing in pooled single-cell RNA-seq and single-cell ATAC-seq experiments. It assigns cells to donors using SNP genotype inf

WASP (Weight And SNP-based Pipeline) corrects allele-specific mapping bias in RNA-seq and ChIP-seq by SNP-masking reads that overlap heterozygous variants, remapping them, and filtering those that shi

wateRmelon v2.16.0 — Bioconductor R package for Illumina 450K and EPIC DNA methylation array normalization and performance metrics. Provides 15 normalization methods (dasen, nasen, naten, danes, swan,

WDL/Cromwell — Workflow Description Language (WDL) authoring and Cromwell execution engine for reproducible bioinformatics pipelines. WDL defines portable, composable workflows using task/workflow blo

wf-basecalling — Oxford Nanopore Technologies (ONT) EPI2ME Nextflow workflow for production-grade basecalling using Dorado. Converts POD5 or FAST5 raw electrical signal files to BAM/FASTQ with optiona

wgbs_tools — command-line toolkit for whole-genome bisulfite sequencing (WGBS) analysis. Converts, indexes, and queries methylation data in efficient PAT/BETA binary formats. Provides per-CpG and per-

WGCNA (Weighted Gene Co-expression Network Analysis) — R package for constructing weighted correlation networks from high-dimensional gene expression data. Identifies co-expression modules via hierarc

Winnowmap — long-read mapping tool optimized for repetitive reference sequences. Uses weighted minimizer sampling and minimal confidently alignable substrings for accurate ONT and PacBio read alignmen

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

WNN (Weighted Nearest Neighbor) — Seurat's method for multimodal single-cell data integration that computes cell-specific modality weights and combines per-modality KNN graphs. Supports any combinatio

ZeroCostDL4Mic is a Google Colab-based platform providing zero-cost deep learning for fluorescence microscopy image analysis. Supports segmentation (U-Net, StarDist, Cellpose), denoising (Noise2Void,

Use when working with bgen — BGEN binary genotype format for large-scale

Combined gwasvcf + ieugwasr routing skill for the IEU OpenGWAS ecosystem. Use when working with OpenGWAS study IDs, GWAS-VCF downloads, local summary statistics querying, LD clumping, proxy lookup, re

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

Use when working with pipeline-composer — pipeline-composer — compose

Protégé is an open-source ontology editor and knowledge graph framework for creating, editing, and reasoning over OWL and RDF ontologies. Use for biomedical ontology development (Gene Ontology, SNOMED

vConTACT2 (Viral Contig Automatic Cluster Taxonomy 2) clusters prokaryotic viral genomes and contigs by shared protein content to assign taxonomy context from reference viral genomes. Use when working

VirSorter2 is a multi-classifier pipeline for identifying DNA and RNA viral sequences from metagenomic and genomic assemblies. It supports dsDNA phage, ssDNA, RNA, NCLDV, and lavidaviridae groups, out

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

GREML (GCTA) — genome-based restricted maximum likelihood analysis for SNP heritability estimation, genetic correlation, mixed linear model association (MLMA), and COJO conditional analysis. Use when

Find drop-in replacements or compatible alternatives for bioinformatics tools using EDAM ontology I/O compatibility matching. Searches 47,000+ tools with curated migration knowledge for 20+ common alt

BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel

Use when working with bgzip — bgzip — BGZF block-compression utility

Docker — container platform for building, running, and distributing reproducible bioinformatics environments. Provides Dockerfile authoring, image management, container execution with volume mounts fo

ENA Browser Tools — EMBL-EBI command-line utilities for programmatic access to the European Nucleotide Archive (ENA). Download FASTQ, SRA, FASTA, EMBL, and submitted files by study, sample, experiment

Use when validating Nextflow pipelines with nf-core/tools lint checks. Routes users to practical guidance for running `nf-core pipelines lint`, selecting targeted tests with `--key`, producing JSON/Ma

NiBabel — Python library for reading and writing neuroimaging file formats. Supports NIfTI-1, NIfTI-2, ANALYZE, MINC1, MINC2, GIFTI, FreeSurfer MGH/MGZ, CIFTI-2, PARREC, and BrainVoyager formats. Core

scipy.optimize — Unified interface for numerical optimization in Python. Provides local and global minimization (minimize, differential_evolution, dual_annealing), root finding (root, root_scalar), cu

TOBIAS — Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal. Python toolkit for differential transcription factor (TF) footprinting from ATAC-seq data. Corrects Tn5 insertio

TreeTime — maximum likelihood molecular clock inference, ancestral sequence reconstruction, and phylodynamic analysis from time-stamped phylogenies. Infers timetrees by iteratively optimizing ancestra

Use when working with vcf2pca — VCF2PCA — lightweight Python tool for

AlleleSeq — pipeline for detecting allele-specific expression (ASE) and allele-specific binding (ASB) from RNA-seq and ChIP-seq data at heterozygous SNP positions. Constructs a personal diploid genome

AMRFinderPlus (NCBI Antimicrobial Resistance Gene Finder Plus) — identifies antimicrobial resistance genes, virulence factors, and stress genes in bacterial genome assemblies and protein sequences. Ac

Use when working with angsd — ANGSD — Analysis of Next Generation Sequencing