Browse Tools

A suite of tools for the MetaboLights open-access metabolomics data repository, including the metabolights-utils Python library and CLI for ISA-Tab file manipulation, study submission, and the mtbls-v

Radiation biology computational toolkit — Linear-Quadratic (LQ) model for cell survival, BED and EQD2 dose-equivalence conversions, clonogenic survival curve fitting, TCP/NTCP modelling, DVH analysis,

Infer bioinformatics file format from magic bytes, header patterns, and file extensions

BLUPF90 suite of programs for mixed model computations, genomic selection, and variance component estimation in animal breeding. Use when working with BLUP/ssGBLUP, genomic EBVs, single-step genomic e

CellTypist — automated cell type annotation for scRNA-seq using logistic regression with pre-trained immune models, majority voting refinement, multi-label classification, custom model training, cross

Use when performing multi-trait colocalization analysis with HyPrColoc to identify shared genetic signals across multiple traits simultaneously. Supports GWAS summary statistics input (beta coefficien

Optogenetics skill for designing, analyzing, and interpreting light-based neural circuit manipulation experiments. Covers opsin selection (ChR2, halorhodopsin, Arch, C1V1, jRCaMP), viral vector strate

pyOpenMS — Python bindings for OpenMS mass spectrometry framework. Read/write mzML, mzXML, mzTab, TraML, and FASTA files. Signal processing, peak picking, feature detection, peptide identification, pr

rMVP GWAS analysis for plant genomics. Use when running genome-wide association studies, GWAS models (GLM, MLM, FarmCPU), SNP genotype formatting, kinship matrix calculation, population structure PCA,

Analyze genetic variants associated with athletic performance, exercise response, injury risk, and trainability. Covers GWAS, polygenic score construction, VO2max heritability, muscle fiber compositio

Use when working with ADMIXTOOLS 2 — the R package for computing f-statistics and modeling population admixture history using ancient and modern DNA. Supports f2, f3, f4, D-statistics, qpAdm (admixtur

AfterQC — automatic filtering, trimming, error removing and quality control for FASTQ data. Processes Illumina paired-end and single-end reads with automatic adapter detection, overlap-based error cor

BioNumPy — NumPy-based Python library for array-oriented genomics analysis.

CNVnator — read-depth (RD) based copy number variation (CNV) detection from whole-genome sequencing BAM/CRAM files. Partitions the genome into equal-size bins, computes normalized read-depth signals,

Use when visualizing functional enrichment results from clusterProfiler, DOSE, or ReactomePA analyses. Covers all major plot types: dotplot for ORA/GSEA overview, barplot for ranked terms, cnetplot fo

FAN-C is a Python framework for analysis, visualization, and exploration of Hi-C and related chromatin conformation capture data. Provides a unified API for importing, processing, and analyzing Hi-C c

FastTree — approximately maximum-likelihood phylogenetic tree inference from nucleotide or protein sequence alignments. Infers large phylogenies (up to 1M sequences) 100-1000x faster than RAxML or Phy

fwdpp is a C++ template library for forward-time population genetic simulation, accessed via its Python bindings fwdpy11. Use when users need to simulate Wright-Fisher diploid populations with selecti

hap.py (Haplotype Comparison Tools) — Python/C++ benchmarking toolkit from Illumina for comparing VCF files against a gold-standard truth set. Computes SNP and INDEL precision, recall, and F1-score fo

HLA*LA — graph-based HLA typing from whole-genome or exome BAM/CRAM files using a Population Reference Graph (PRG) of the MHC region. Calls HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQB1, HLA-DPB1, and six a

'Use when working with instrain — inStrain — strain-level microbial population

Use when working with krakenuniq — krakenUniq — metagenomics taxonomic

MEME Suite — motif-based sequence analysis toolkit for de novo motif discovery (MEME, STREME), motif enrichment testing (AME, SEA, CentriMo), motif scanning (FIMO, MAST, MCAST), motif comparison (Tomt

NCO (netCDF Operators) is a suite of command-line programs that manipulate and analyze data stored in netCDF-accessible formats, including DAP, HDF4, HDF5, and Zarr. Primary use cases include metadata

Nipy — Python library for neuroimaging analysis with a focus on fMRI preprocessing and statistical modeling. Provides motion correction via SpaceTimeRealigner, slice timing correction, image registrat

Use when working with PhiSpy — prophage identification in annotated bacterial genomes using machine learning and genomic composition. PhiSpy combines protein similarity to known phage proteins (via HM

Primer3 — the standard primer design engine for PCR, sequencing, cloning, and hybridization probe applications. Designs oligonucleotide primers from DNA template sequences with full thermodynamic cont

PyPGx is a Python package and CLI for pharmacogenomics (PGx) analysis — star allele genotyping of pharmacogenes from next-generation sequencing (NGS) or genotyping chip data. Supports 80+ pharmacogene

R2DT (RNA 2D Templates) — draws RNA secondary structures in consistent, publication-quality orientations using template-based layout. Given RNA sequences in FASTA format, R2DT searches 4,500+ Rfam cov

ROSE (Rank Ordering of Super-Enhancers) — identifies super-enhancers from ChIP-seq data by stitching constituent enhancers within a genomic window, ranking by signal density, and finding the inflectio

Use when working with slivar — slivar — fast VCF/BCF variant filtering

STARRPeaker — covariate-corrected STARR-seq peak caller from the Gerstein Lab. Detects active regulatory regions (enhancers, promoters) from paired-end STARR-seq BAM files by modeling systematic biase

Struo2 — Snakemake pipeline for building custom Kraken2, Bracken, and HUMAnN3 databases from NCBI or GTDB genome accessions. Automates downloading reference genomes, formatting taxonomy, and running K

Ubergraph — integrated biomedical ontology knowledge graph built from ~100 OBO ontologies (GO, UBERON, CL, HP, MP, CHEBI, RO, and more) with pre-materialized OWL reasoning. Query the public SPARQL end

Use when working with V-pipe, the Snakemake workflow for within-sample viral sequencing analysis from Illumina or similar NGS reads. V-pipe organizes samples in a two-level directory hierarchy, suppor

ECMWF ai-models — unified CLI and Python framework for running AI-based weather forecasting models including PanguWeather, FourCastNet, FourCastNetv2, and GraphCast. Provides standardized input handli

Amelia II — R package for multiple imputation of incomplete multivariate data using a bootstrap-based EM algorithm (EMB). Faster and more scalable than MCMC approaches, with native support for time-se

AntiFold — antibody-specific inverse folding model built on ESM-IF1, fine-tuned on antibody structures from SAbDab and OAS databases. Predicts residue log-likelihoods for antibody variable domains (IM

ASTRAL — fast species tree estimation from unrooted gene trees under the multi-species coalescent model. Handles incomplete lineage sorting (ILS) in phylogenomic datasets with hundreds of species and

10x Genomics bamtofastq — converts Cell Ranger, Space Ranger, and Visium BAM files back to FASTQ format, preserving cell barcodes (CB), UMIs (UB), and read structure for re-processing with updated pip

TODO: Add a comprehensive description for betapart. Explain its purpose, what it does, and its primary functionalities related to beta diversity.

BiodiversityR — R package for biodiversity and community ecology analysis: species richness, diversity indices (Shannon, Simpson, Fisher's alpha), rank-abundance dominance (RAD) curves, species accumu

BioGPT — domain-specific generative pre-trained transformer for biomedical text mining and generation, pre-trained on 15M+ PubMed abstracts. Supports biomedical text generation, relation extraction, q

Bookdown for long-form technical writing with R Markdown. Use this skill when users need to author books, reports, or documentation with chapter cross-references, theorem/equation numbering, citations

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Use when correcting copy-number bias in CRISPR-Cas9 essentiality screens with CERES. Handles guide-level depletion data from Project Achilles or custom CRISPR knockout screens, integrating segmented c

CHOPCHOP — web-based and command-line tool for designing optimized CRISPR guide RNAs (sgRNA) and TALENs. Supports Cas9, Cas9 nickase, Cpf1/Cas12a, and Cas13 nuclease systems across 200+ genomes. Provi