Browse Tools

iheatmapr — rOpenSci R package for building interactive, multi-panel complex heatmaps powered by plotly. Constructs modular iheatmap S4 objects by chaining add_* functions: add_col_signal, add_row_sig

In-silico PCR (isPCR) simulates PCR amplification computationally by searching a genome or sequence database for products defined by primer pairs. Use for primer specificity checking, amplicon predict

Use this skill for Inkscape command-line figure workflows: SVG cleanup, deterministic exports (PNG/PDF/PS/EPS), batch rendering with --actions, geometry queries, and publication-figure validation. Tri

Inspector — long-read-based genome assembly evaluation and error correction. Use for: assembly quality assessment, QV (quality value) score calculation, structural error detection, small-scale error p

Illumina InterOp is a C++ library with Python and C# bindings for reading InterOp metric files emitted by Illumina sequencers and Sequencing Analysis Viewer workflows. Use this skill when you need to

Sequence analysis application that combines multiple protein signature databases to annotate proteins with functional domains, sites, and families.

Use this skill for ITK (Insight Segmentation and Registration Toolkit), the C++/Python library for medical image segmentation, registration, and filtering. Covers itk Python API for image I/O (DICOM,

Use when extracting ITS (Internal Transcribed Spacer) regions from rRNA sequences for fungal, plant, or microbial metabarcoding. Covers ITS1/ITS2 extraction, taxonomic domain filtering, FASTA output f

Use when working with iVar for viral amplicon sequencing, primer trimming, intrahost variant calling, consensus generation, replicate-aware variant filtering, or primer mismatch masking workflows. iVa

Use when performing comparative genomics synteny analysis with JCVI/MCscan, the Python toolkit for detecting and visualizing collinear gene blocks between plant or fungal genomes. Covers ortholog iden

Use when working with JGI MycoCosm, the DOE Joint Genome Institute fungal genomics portal. Covers downloading fungal genome assemblies, gene annotations, and proteomes from the MycoCosm database; prog

Use when working with Jovian for viral metagenomics or viromics from raw paired-end Illumina FASTQ data in public-health, clinical, or batch sequencing contexts. Jovian is a Snakemake-based workflow t

Juicer — one-click Hi-C data processing pipeline that aligns paired-end FASTQ reads to a reference genome and produces .hic contact matrices for chromatin conformation analysis. Handles alignment (BWA

UCSC kent-core — standalone C command-line tools for genome browser data processing. Covers liftOver (coordinate remapping between assemblies), bigWig/bigBed creation and querying, 2bit format convers

UCSC Kent utilities (kent-core) — a collection of C command-line tools for genome browser data processing. Covers liftOver (coordinate remapping between assemblies), bigWig/bigBed creation and queryin

LDAK — LD-adjusted kinship toolkit for SNP heritability estimation, genetic architecture analysis, and genomic prediction. Computes LDAK-Thin and LDAK-GCTA kinship matrices, estimates per-chromosome a

LEA (Landscape and Ecological Association studies) is an R/Bioconductor package for population structure analysis and environmental/ecological genomics. Performs sparse NMF (sNMF) for ancestry estimat

libBigWig — C library and pyBigWig Python bindings for reading and writing BigWig and BigBed binary indexed genome browser track files. Use when users need to extract signal values, interval statistic

Use when performing differential gene expression analysis on RNA-seq count data using limma-voom. Covers the full workflow: count filtering with filterByExpr, TMM normalization via edgeR calcNormFacto

LipidFinder routing skill for lipidomics LC-MS feature filtering and lipid annotation. Use this skill when users mention LipidFinder, LipidSearch, LIPID MAPS, LMSD, lipidomics feature annotation, lipi

LipidSig routing skill for lipidomics data analysis. Use this skill when users mention LipidSig, lipid species profiling, lipid class enrichment, differential lipid analysis, lipidomics volcano plots,

LJA (La Jolla Assembler) — de novo genome assembler for PacBio HiFi (CCS) long reads using a multiplex de Bruijn graph that simultaneously spans multiple k-mer lengths. Produces chromosome-scale, high

Use when working with LoFreq for sensitive SNV or indel calling from aligned next-generation sequencing data, especially viral quasispecies, bacterial resequencing, targeted panels, exomes, or matched

Long Ranger is 10x Genomics software for processing linked-read sequencing data from the Chromium Genome and Exome kits. Use this skill when users need to run `longranger wgs` for whole-genome phased

LTR_retriever — command-line Perl tool for high-accuracy identification of Long Terminal Repeat retrotransposons (LTR-RTs) in plant and eukaryotic genomes. Filters raw LTRharvest and LTR_FINDER candid

Maftools — R package for analyzing somatic mutations from cancer sequencing (MAF files). Provides oncoplots for mutation visualization, clonality analysis, tumor burden estimation, mutational signatur

MalariaGEN data Python package for accessing and analysing malaria genomic epidemiology data. Provides cloud-native APIs for Anopheles mosquito vectors (Ag3, Af1, Amin1, Adir1) and Plasmodium parasite

MASS — Modern Applied Statistics with S. R package providing negative binomial GLMs via glm.nb(), robust linear models via rlm() with Huber/bisquare/Hampel psi functions, linear and quadratic discrimi

MatrixEQTL — ultra-fast R package for eQTL, sQTL, and pQTL mapping using large matrix operations. Supports cis and trans analysis with linear and ANOVA models, multiple covariates, and FDR-corrected o

MaveDB utilities — search, download, and process variant effect scores from the MaveDB database of multiplexed assay for variant effect (MAVE) experiments. Supports fetching ScoreSets, Experiments, an

Use when processing highly multiplexed tissue images with MCMICRO, the end-to-end Nextflow pipeline for CyCIF, CODEX, mIHC, and other cyclic immunofluorescence imaging modalities. Covers illumination

Use when detecting synteny, collinearity, or gene duplication events between plant genomes or any pair of sequenced genomes with MCScanX. Covers input preparation (BLAST + GFF), running MCScanX collin

Use when working with MENDER (MultilayEred NeighborhooDhood-Encoded Representations), a Python tool for spatial domain identification in multiplexed imaging data. Covers spatial domain segmentation in

Use when working with MetaMaps for long-read metagenomic read assignment, strain-level composition estimation, or database-guided taxonomic profiling. MetaMaps combines approximate long-read mapping w

Minigraph — sequence-to-graph aligner and incremental pangenome graph assembler for long reads and whole-genome assemblies. Aligns PacBio/ONT reads or haplotype-resolved assemblies to an rGFA referenc

MiXCR — full-featured immune repertoire analysis from raw FASTQ to clonotype tables. Align paired-end or single-end reads to V(D)J reference genes (TCR alpha/beta/gamma/delta, BCR heavy/light), assemb

MNE-Python — open-source EEG, MEG, and iEEG data analysis for neuroscience and brain imaging. Process raw electrophysiology recordings: filtering, epoching, artifact rejection with ICA, event-related

Use when working with MONAI — the Medical Open Network for AI — a PyTorch-based framework for deep learning in medical imaging. Covers 3D image segmentation, classification, detection, and reconstruct

Monocle3 trajectory inference and pseudotime analysis for single-cell RNA-seq in R/Bioconductor. Use when users need principal-graph trajectory learning, pseudotime ordering, trajectory-dependent gene

MPRAflow — Snakemake pipeline for Massively Parallel Reporter Assay (MPRA) data from the Shendure Lab. Handles barcode-sequence association, DNA/RNA barcode counting, activity score computation (RNA/D

MPRAnator — web and command-line tool for designing Massively Parallel Reporter Assay (MPRA) oligonucleotide libraries. Tiles input sequences (enhancers, regulatory elements, SNP-containing loci) into

mpraprofiler — MPRA (Massively Parallel Reporter Assay) data analysis tool for quantifying regulatory element activity from barcode count tables. Normalizes DNA and RNA counts, computes activity ratio

MR-Egger is an R-based Mendelian randomization method that estimates causal effects from GWAS summary statistics while allowing directional pleiotropy via an unconstrained intercept term. Use when tes

Use when working with MRInstruments — an R package for retrieving and curating genetic instrument variables for Mendelian randomization (MR) analyses. Provides access to GWAS summary statistics, clump

MRMix is an R package for Mendelian randomization analysis using a two-component Gaussian mixture model to account for horizontal pleiotropy. Use when estimating causal effects from GWAS summary stati

MS-DIAL — open-source software from RIKEN for untargeted metabolomics and lipidomics data processing. Provides deconvolution, peak picking, alignment, isotope and adduct annotation, compound identific

msigdbr — R package providing MSigDB (Molecular Signatures Database) gene sets as tidy data frames for use in gene set enrichment analysis (GSEA), over-representation analysis (ORA), and pathway analy

MSnbase routing skill for R/Bioconductor mass spectrometry data handling, preprocessing, and quantification. Use this skill when users mention MSnbase, MSnExp, OnDiskMSnExp, MSnSet, LC-MS/MS preproces

msprime is a coalescent simulator for population genetics that generates tree sequences and ARGs under the Wright-Fisher and other models. Use when users need to simulate genetic variation under demog

MultiVI — deep generative model for joint analysis of scRNA-seq and scATAC-seq multi-omics data using variational inference. Part of scvi-tools (scverse ecosystem). Integrates single-modality and mult