Browse Tools

limma-voom — linear models for differential expression analysis of RNA-seq and microarray data. The voom transformation converts RNA-seq read counts to log-CPM with precision weights derived from the

LinusFold — IBM Research protein structure prediction tool that uses a protein language model to predict 3D structures from amino acid sequences. Accepts FASTA input and produces PDB/mmCIF coordinate

LongQC — quality control tool for long-read sequencing data from Oxford Nanopore and PacBio platforms. Generates comprehensive QC reports with read length distributions, per-read quality scores, cover

Use when working with loompy — loompy — Python library for reading, writing,

LotuS2 (Less OTU Scripts 2) — ultrafast amplicon sequencing pipeline for 16S, 18S, 23S, 28S, and ITS marker gene analysis of microbial communities. Processes raw FASTQ/FASTA through demultiplexing (sd

Magic-BLAST — NCBI aligner for mapping large next-generation RNA or DNA sequencing runs against whole genomes or transcriptomes. Optimizes composite paired-read scores with splice-aware alignment, exc

MaizeGDB (Maize Genetics and Genomics Database) — the community database for maize (Zea mays) genetics and genomics. Query gene models, loci, QTLs, traits, germplasm, and metabolites via the MaizeGDB

Use when working with malacoda — an R package for Bayesian analysis of Massively Parallel Reporter Assay (MPRA) data. Quantifies transcriptional regulatory element activity from barcode count data usi

Use when working with MAST — an R/Bioconductor package for differential expression analysis of single-cell RNA-seq data. Fits a hurdle model (zero-inflated two-component regression) via zlm() to handl

Matplotlib — comprehensive Python library for creating static, animated, and interactive visualizations. Provides publication-quality figures with fine-grained control over every plot element via the

MaxQuant — quantitative proteomics platform for analyzing large-scale mass spectrometry data. Integrates the Andromeda search engine for peptide identification, supports label-free quantification (LFQ

MEGA (Molecular Evolutionary Genetics Analysis) — cross-platform software suite for phylogenetic tree construction, multiple sequence alignment, molecular evolution analysis, and molecular dating. Sup

Megalodon — Oxford Nanopore basecalling-anchored analysis tool for modified base detection (5mC, 5hmC, 6mA) and sequence variant calling from raw nanopore signal (FAST5) data. Provides per-read and pe

Use when working with MEGAN (MEtaGenome ANalyzer) or MEGAN-CE — interactive exploration and taxonomic/functional classification of metagenome sequencing data. Applies the LCA (Lowest Common Ancestor)

MELD (Manifold Enhancement of Latent Dimensions) -- Python package for quantifying the effect of experimental perturbations at single-cell resolution. Uses graph signal processing to estimate sample-a

Meryl — fast k-mer counting and set-operation toolkit from the Marbl group (Canu/Verkko). Counts canonical or strand-specific k-mers from FASTA/FASTQ inputs into binary meryl databases, then supports

Mesmer — deep learning-powered whole-cell segmentation for multiplexed tissue imaging. Uses a pre-trained TissueNet model to segment both nuclei and whole cells from multiplex fluorescence images (COD

MetaboAnalyst — comprehensive R package and web platform for metabolomics data analysis and interpretation. Provides statistical analysis (t-test, ANOVA, PCA, PLS-DA), pathway analysis (KEGG, SMPDB),

MetaCell is the original Tanay lab R package for building metacells from single-cell RNA-seq UMI matrices by partitioning a balanced cell similarity graph into small homogeneous groups. Use it for 10x

methylpy — Python pipeline for whole-genome bisulfite sequencing (WGBS) methylation analysis. Trims adapters, aligns with Bowtie2, marks duplicates, and calls cytosine methylation in CpG, CHG, and CHH

MGI/GXD (Mouse Genome Informatics / Gene Expression Database) — authoritative resource for mouse genetics, genomics, and gene expression data maintained by The Jackson Laboratory. Provides comprehensi

MicrobiomeAnalystR — comprehensive R package for statistical analysis of microbiome data from 16S rRNA amplicon sequencing and shotgun metagenomics. Provides alpha diversity (Shannon, Chao1, ACE, Fait

Use when working with microeco — an R6-class R package for microbiome community ecology analysis. Handles OTU/ASV tables, taxonomy, sample metadata, and phylogenetic trees in a unified microtable obje

miloR — R/Bioconductor package for differential abundance (DA) testing on single-cell datasets using k-nearest neighbor (KNN) graphs. Identifies cell populations that shift in frequency across experim

mixOmics — R/Bioconductor package for multi-omics data integration using multivariate projection methods. Provides PCA, PLS, sPLS, PLS-DA, sPLS-DA, DIABLO (multi-block sPLS-DA), and MINT (multi-study

MOFA+ (Multi-Omics Factor Analysis) — Bayesian group factor analysis framework for unsupervised integration of multiple omics data modalities. Discovers shared and modality-specific latent factors fro

MPRAnalyze -- R/Bioconductor package for Massively Parallel Reporter Assay (MPRA) analysis. Uses a parametric graphical model on raw DNA/RNA count matrices to quantify enhancer-induced transcription r

Use when running Massively Parallel Reporter Assay (MPRA) data analysis with MPRAsnakeflow. Covers barcode-sequence association, barcode count quantification, activity score calculation (RNA/DNA ratio

mr.ash (Multiple Regression with Adaptive Shrinkage) is an R package that fits sparse Bayesian multiple regression models using variational Bayes EM with adaptive shrinkage (ash) priors. Designed for

MsCAVIAR (Multiple Summary Statistics CAVIAR) — Bayesian statistical fine-mapping tool for GWAS loci using multiple traits/phenotypes simultaneously. Computes posterior inclusion probabilities (PIPs)

MSstats — Bioconductor R package for statistical analysis of quantitative mass spectrometry-based proteomics experiments. Supports label-free DDA, TMT, iTRAQ, SRM/MRM, and DIA workflows. Provides prep

MuData — Python multimodal data container for storing and manipulating multi-omics single-cell datasets built on AnnData. Provides MuData objects wrapping multiple AnnData modalities (RNA, ATAC, prote

Muon — multimodal omics data analysis framework from the scverse ecosystem. Built on the MuData container for multi-modal single-cell experiments including CITE-seq, Multiome (RNA+ATAC), TEA-seq, and

Use when working with muscat — the Bioconductor R package for multi-sample multi-condition differential state (DS) analysis of single-cell RNA-seq data. Performs pseudo-bulk aggregation (aggregateData

MutationalPatterns — R/Bioconductor package for comprehensive analysis of somatic mutational patterns in cancer genomes. Extracts and visualizes mutational signatures (SBS, DBS, indel), performs COSMI

MutPred2 — machine learning pathogenicity predictor for amino acid substitutions (missense variants). Generates a pathogenicity score (0–1) and ranked molecular mechanism hypotheses (loss/gain of PTMs

MZmine 3 — open-source Java software for LC-MS and GC-MS mass spectrometry data processing in untargeted metabolomics. Provides feature detection (ADAP, local minimum), chromatogram building, isotope

ncbi-genome-download is a Python CLI tool and library for bulk downloading genome sequences and associated files from NCBI RefSeq and GenBank FTP servers. Supports all taxonomic groups (bacteria, fung

Nextclade — viral genome alignment, clade/lineage assignment, mutation calling, and sequence quality assessment. Aligns query sequences against pathogen-specific reference datasets (SARS-CoV-2, influe

nf-core — community-curated Nextflow pipeline framework with 100+ production bioinformatics pipelines. Provides CLI tools for listing, launching, downloading, creating, and linting pipelines; managing

nf-core/atacseq — Nextflow pipeline for ATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) data analysis. Handles paired- or single-end reads through adapter trimming (Trim Galore),

nf-core/mag — Nextflow pipeline for metagenome-assembled genome (MAG) analysis. Takes raw short-read (Illumina) and/or long-read (Nanopore/PacBio) metagenomic sequencing data through quality control,

Octopus — Bayesian haplotype-based variant caller for germline and somatic mutation detection from WGS, WES, and targeted sequencing data. Supports multiple calling models including individual, trio,

ome-zarr-py -- Python library for reading and writing OME-Zarr (NGFF) images, the cloud-native, chunked, multiscale format for bioimaging. Provides APIs for reading OME-Zarr datasets with multiscale p

Use when working with OmegaFold to predict 3D protein structures from amino acid sequences without multiple sequence alignments (MSA-free). Covers single-sequence structure prediction, batch FASTA pro

OMERO (Open Microscopy Environment Remote Objects) — client-server platform for managing, visualizing, and analyzing microscopy image data. Provides centralized image repository with Python API (omero

OMIM API — programmatic access to the Online Mendelian Inheritance in Man database of human genes and genetic phenotypes. Supports entry lookup by MIM number, full-text search, gene map queries, clini

OmniPath and OmnipathR — systems biology prior knowledge database and R client for accessing protein-protein interactions, gene regulatory networks, enzyme-substrate (PTM) relationships, protein compl

OncoKB — precision oncology knowledge base from Memorial Sloan Kettering

Open Targets Platform — large-scale target identification and prioritization resource integrating genetic, genomic, and disease evidence for drug target discovery. Provides REST API and Python client