Browse Tools

REViewer — haplotype-resolved visualization of read alignments at short tandem repeat (STR) loci detected by ExpansionHunter. Accepts a sorted BAM/CRAM file, an ExpansionHunter VCF, a reference FASTA,

RoseTTAFold — deep learning-based protein structure prediction using a three-track neural network architecture for simultaneous processing of 1D sequence, 2D distance maps, and 3D coordinates. Predict

cgpBattenberg (Sanger Institute) detects allele-specific copy number alterations and subclonal copy number aberrations in cancer whole-genome sequencing data. Implements the Battenberg algorithm using

SemiBin — semi-supervised metagenomic binning using deep learning with self-supervised contrastive learning for contig embeddings. Supports single-sample, multi-sample, and long-read binning modes. Sh

Singularity/Apptainer — HPC container runtime for building, running, and managing SIF container images in rootless, multi-tenant cluster environments. Provides OCI-compatible builds from Dockerfiles a

slow5tools -- command-line toolkit for converting, compressing, merging, splitting, indexing, and extracting reads from SLOW5/BLOW5 format files. SLOW5/BLOW5 is an alternative to HDF5-based FAST5/POD5

Use when working with SMINA — a fork of AutoDock Vina with improved scoring functions and flexible docking for structure-based virtual screening and lead optimization. SMINA extends Vina with custom s

SnpSift -- Java-based toolset for filtering, annotating, and manipulating annotated VCF files from SnpEff or other variant callers. Provides expression-based filtering (filter), database annotation wi

sourmash — fast k-mer sketching and comparison for genomic and metagenomic data using FracMinHash (scaled MinHash). Computes DNA and protein sketches, performs pairwise genome comparison, containment

Use when working with stranger — a Clinical Genomics tool for annotating short tandem repeat (STR) variants in VCF files with pathogenicity classifications. Accepts VCFs from ExpansionHunter or TRGT a

Tandem-genotypes — genotype tandem repeats from long-read sequencing alignments. Analyzes minimap2 or LAST alignments against tandem-repeats-finder annotations to call insertion/deletion lengths at ta

TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a Java-based software package for genome-wide association studies (GWAS), population genetics, and linkage disequilibrium analysis. Su

Toil is a Python workflow execution engine for reproducible, scalable biomedical data analysis. Supports CWL, WDL, and Python-native workflows on local machines, HPC clusters (SLURM, LSF, Grid Engine,

Trimmomatic — flexible, multithreaded read trimming tool for Illumina sequence data. Performs adapter removal (palindrome and simple modes), quality trimming (sliding window, leading/trailing), hard c

Truvari — structural variant benchmarking, merging, and annotation toolkit for VCF files. Provides SV caller performance evaluation (bench) with configurable size/sequence/overlap thresholds, redundan

wigToBigWig converts Wiggle (.wig) format files — fixedStep and variableStep — to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-s

xarray-spatial — fast Numba-accelerated Python library for raster spatial analysis operations on xarray DataArrays. Provides surface analysis (slope, aspect, curvature, hillshade, viewshed), focal sta

Analyze bioinformatics sample metadata to auto-detect data modality, column semantics, and sequencing platform from CSV/TSV files, SRA RunTables, GEO Series Matrix files, and AnnData .obs exports. Inf

Use when working with Ankh — an optimized protein language model — for generating protein sequence embeddings, secondary structure prediction, remote homology detection, and protein property predictio

ANNOVAR — efficient Perl-based tool for functional annotation of genetic variants from diverse genomes. Supports gene-based, region-based, and filter-based annotation using 100+ databases including Cl

Arvados — open-source platform for managing, processing, and sharing large biomedical datasets at scale. Combines Keep (content-addressable distributed storage), Crunch (container-based compute dispat

Use when working with ASEQ — Allele-Specific Expression Quantification — an R command-line tool for detecting allelic imbalance from RNA-seq data. Counts reference and alternative allele reads at hete

Auspice — interactive visualization tool for phylogenomic and genomic epidemiology data from the Nextstrain platform. Renders Nextstrain JSON datasets as interactive phylogenetic trees, geographic tra

Bakta — rapid, standardized annotation of bacterial genomes, plasmids, and metagenome-assembled genomes (MAGs). Provides comprehensive feature detection (CDS, tRNA, rRNA, ncRNA, CRISPR, sORF, oriC/ori

ballgown -- R/Bioconductor package for flexible isoform-level differential expression analysis of RNA-seq experiments. Works with StringTie output (.ctab files) to test for differential expression at

Use when working with batchelor — the Bioconductor R package for batch correction of single-cell RNA-seq data. Removes batch effects using mutual nearest neighbours (fastMNN, mnnCorrect), linear resca

Battenberg is an R package for allele-specific subclonal copy number analysis from whole-genome sequencing (WGS) tumor/normal paired BAM files. It segments the genome into clonal and subclonal copy nu

Bioconductor package management and installation via BiocManager for R-based genomic data analysis. Install, update, and validate Bioconductor packages for RNA-seq, ChIP-seq, single-cell, methylation,

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

BioJulia — Julia ecosystem for computational biology providing high-performance biological sequence analysis, file I/O for FASTA/FASTQ/BAM/SAM/VCF/GFF3 formats, pairwise alignment, genomic interval op

Biostrings — Bioconductor R package for efficient manipulation of biological sequences (DNA, RNA, amino acids). Provides S4 classes DNAStringSet, RNAStringSet, AAStringSet for collections; pattern mat

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

Use when working with Borzoi — a sequence-to-function DNA foundation model — for predicting genome-wide regulatory activity from DNA sequences. Borzoi predicts RNA-seq, ATAC-seq, ChIP-seq, and histone

Use when analyzing EEG or MEG electrophysiology data with Brainstorm. Covers preprocessing (filtering, artifact rejection, ICA), source reconstruction (MNE, beamformer, dipole fitting), time-frequency

bsseq -- Bioconductor R package for analyzing and visualizing bisulfite sequencing (BS-seq) data, including whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RR

btrack is a Bayesian multi-object cell tracking library for time-lapse microscopy data. Tracks individual cells across frames using a Bayesian belief matrix and motion model. Integrates natively with

bwa-meth -- fast and accurate bisulfite-seq (WGBS/RRBS) aligner built on BWA-MEM. Performs in-silico C-to-T conversion of reads and reference, aligns with BWA-MEM or BWA-MEM2, and recovers original ba

CADD (Combined Annotation Dependent Depletion) -- integrative framework for scoring the deleteriousness of single nucleotide variants and insertion/deletions in the human genome. Combines diverse geno

CARE (Content-Aware Image Restoration) is a deep learning framework for fluorescence microscopy image enhancement using convolutional neural networks. Restores noisy, low-SNR microscopy images through

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

cell2location — Bayesian spatial deconvolution mapping fine-grained cell types from scRNA-seq references onto spatial transcriptomics data. Estimates absolute cell type abundance per location via Pyro

CellChat — R package for inference, analysis, and visualization of cell-cell communication networks from single-cell RNA-seq data. Uses a curated ligand-receptor database (CellChatDB) to quantify sign

CellOracle — Python toolkit for gene regulatory network (GRN) inference and in silico transcription factor (TF) perturbation simulation from single-cell data. Builds cluster-specific GRNs by integrati

Cellpose — generalist deep learning algorithm for cellular and nuclear segmentation in microscopy images. Provides GPU-accelerated 2D and 3D instance segmentation using gradient flow representations,

Use this skill for CellRank 2 fate mapping workflows in single-cell data. CellRank combines transition kernels (for example RNA velocity, pseudotime, CytoTRACE, connectivity, or experimental time) wit

Use when working with CellRegMap — a Python framework for mapping context-specific genetic effects (sc-eQTL) in single-cell RNA-seq data. CellRegMap models genotype × cell-state interactions using a l

chainTools (UCSC Kent utilities) — command-line suite for manipulating genome pairwise alignment chain and net files produced by LASTZ, BLAT, and other whole-genome aligners. Use when users need to so

Change-O is the Immcantation toolkit for B cell immunoglobulin repertoire analysis. Parse IMGT/IgBLAST V(D)J alignment output into AIRR-format databases with MakeDb.py, cluster sequences into clonotyp

CheckM — assess the quality of microbial genomes recovered from metagenomes, single cells, and isolates. Estimates genome completeness and contamination using lineage-specific sets of single-copy mark