Browse Tools

Tools for manipulating next-generation sequencing data stored in SAM/BAM/CRAM format, including sorting, indexing, and format conversion.

Ensembl VEP (Variant Effect Predictor) — annotates genomic variants with gene, transcript, protein, and regulatory consequences using Ensembl's annotation framework. Supports VCF, HGVS, and genomic co

Differential expression analysis for RNA-seq data using negative binomial generalized linear models with size factor normalization and empirical Bayes shrinkage.

Deep learning system for protein structure prediction from amino acid sequence with atomic accuracy — revolutionized structural biology.

Spliced Transcripts Alignment to a Reference — ultrafast RNA-seq aligner with splice junction detection and novel transcript discovery.

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

Data-driven computational pipeline framework enabling scalable and reproducible scientific workflows using software containers.

Aggregate bioinformatics analysis results from many samples and tools into a single report — supports 150+ tools including FastQC, STAR, HISAT2, and Samtools.

Java command-line tools from the Broad Institute for manipulating high-throughput sequencing data and formats including BAM, CRAM, and VCF.

Biosequence analysis using profile hidden Markov models — for detecting remote homologs, protein domain identification, and multiple sequence alignments.

Versatile sequence alignment program for mapping long reads (PacBio/Oxford Nanopore), splice-aware RNA-seq alignment, and assembly-to-assembly alignment.

Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.

Near-optimal probabilistic RNA-seq quantification using pseudoalignment against transcriptome index — orders of magnitude faster than traditional aligners.

BEDTools — Swiss-army knife for genome arithmetic on genomic intervals. Provides intersect, merge, subtract, complement, closest, window, coverage, genomecov, slop, flank, sort, groupby, getfasta, mas

Removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Rapid prokaryotic genome annotation tool producing standards-compliant GFF3, GenBank, and FASTA output for submission and downstream analysis.

Metagenomic phylogenetic analysis tool for profiling microbial community composition from shotgun metagenomics data using clade-specific markers.

Multiple sequence alignment tool with high accuracy and high throughput — one of the best-performing multiple alignment programs.

Use when performing GWAS fine-mapping with PAINTOR (Probabilistic Annotation INTegratOR). Computes posterior inclusion probabilities (PIPs) for causal variants by integrating summary statistics (Z-sco

SBayesR and SBayesRC are Bayesian methods for polygenic risk score (PRS) computation, SNP heritability estimation, and genetic architecture analysis using GWAS summary statistics and an LD reference p

>

Efficient transcript assembly and quantification from RNA-seq alignments using a network flow algorithm with optional guide annotation.

Use when working with CVXPY — a Python-embedded domain-specific language for convex optimization problems. Covers problem construction with the DCP (Disciplined Convex Programming) ruleset, all built-

Use when filtering or subsampling long reads (Oxford Nanopore, PacBio) by quality, length, or target coverage depth. Filtlong selects the best reads from a set rather than random reads, using quality

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

rioxarray is a geospatial xarray extension powered by rasterio that adds a `.rio` accessor to DataArray and Dataset objects, enabling CRS management, reprojection, clipping, resampling, and GeoTIFF/Ne

nc-time-axis provides cftime-aware axis support for matplotlib, enabling the plotting of time series that use non-standard calendars (360_day, noleap, all_leap, julian, etc.) common in climate, weathe

Use when working with Crux — the University of Washington Noble Lab's open-source toolkit for bottom-up tandem mass spectrometry (MS/MS) proteomics analysis. Covers the full peptide identification pip

PyDESeq2 — Python implementation of DESeq2 for differential gene expression analysis from bulk RNA-seq count data. Performs size factor normalization, genewise dispersion estimation, Wald tests with B

M-CAP (Mendelian Clinically Applicable Pathogenicity) is a clinical-grade pathogenicity classifier for rare human missense variants. Developed at the Bejerano Lab (Stanford), it applies a gradient-boo

openTSNE — modular Python library for t-distributed Stochastic Neighbor Embedding. Implements Barnes-Hut and FIt-SNE (interpolation-based) acceleration for scalable O(n log n) / near-linear t-SNE on l

Satpy is a Python library for reading, manipulating, and writing meteorological remote sensing data from various satellite instruments. It is part of the PyTroll project.

sdm (R) is a reproducible framework for species distribution modelling (SDM) that unifies data preparation, multi-method model fitting, evaluation, ensemble forecasting, and spatial/temporal predictio

Sentinel Hub is a cloud-based satellite imagery access and processing platform that provides programmatic access to Copernicus Sentinel, Landsat, MODIS, and commercial satellite data collections throu

SourceTracker2 is a Bayesian microbial source-tracking tool that estimates source contributions to sink communities using Gibbs sampling. Use this skill for SourceTracker/SourceTracker2 workflows, mic

BCFtools — comprehensive toolkit for manipulating variant calls in VCF and BCF format. Provides variant calling (mpileup + call), filtering, querying, merging, concatenation, normalization, annotation

Apollo (Genome Architect) — collaborative, web-based genome annotation editor for manual curation of gene models. Embeds a JBrowse-based genome browser with real-time multi-user annotation editing via

BLAT (BLAST-Like Alignment Tool) is a rapid sequence alignment tool from the UCSC Genome Browser group for aligning mRNA, EST, or DNA sequences to a reference genome. Optimized for highly similar sequ

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

GATK (Genome Analysis Toolkit) — the industry-standard framework for variant discovery in high-throughput sequencing data. Covers the gatk command-line wrapper, Java/JVM tuning, resource bundle manage

Molecular Transformer is an open-source sequence-to-sequence Transformer model (OpenNMT-py) for data-driven chemical reaction prediction and retrosynthesis planning. Trained on USPTO reaction datasets

nebula is an R package for large-scale differential gene expression (DGE) analysis of single-cell RNA-seq data using negative binomial mixed models (NBMM). Implements the NEBULA method (NEgative Binom

Open Data Cube (ODC) is an open-source geospatial data management and analysis framework that indexes Earth observation satellite imagery and gridded datasets into a PostgreSQL catalogue and exposes t

Use when working with Trycycler — a tool for generating consensus long-read genome assemblies from multiple assemblies of the same sample. Combines outputs from assemblers such as Flye, Miniasm, Raven

Use when working with Convex.jl — a Julia package for Disciplined Convex Programming (DCP) that formulates and solves convex optimization problems with natural mathematical syntax. Covers problem cons

rjags is the canonical R interface to JAGS (Just Another Gibbs Sampler), providing R functions for compiling BUGS-language models, running adaptive and burn-in phases, and drawing posterior samples as

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.

Spectral Python (SPy) routing skill for hyperspectral image data representation, manipulation, and processing. Use this skill when users mention SPy, spectralpython, hyperspectral imagery, ENVI header

xESMF — Regrid geospatial and climate datasets between structured grids using ESMF (Earth System Modeling Framework). Use when working with climate model output (CMIP6, ERA5, CESM), satellite data, or