Browse Tools

FragPipe/MSFragger — ultrafast proteomics database search engine and computational pipeline for peptide identification from mass spectrometry (MS/MS) data. Supports closed search, open search for post

FUMA (Functional Mapping and Annotation of Genome-Wide Association Studies) maps GWAS summary statistics to genes and biological functions via three complementary strategies: positional mapping, eQTL

gamlss — Generalized Additive Models for Location, Scale and Shape in R. Distributional regression framework that models all parameters of a response distribution (location mu, scale sigma, skewness n

Use when running GATK Mutect2 for somatic SNV and indel detection, low allele frequency (low AF) variant calling, tumor-normal paired somatic mutation analysis, tumor-only somatic calling, panel of no

GCTA (Genome-wide Complex Trait Analysis) — command-line tool for estimating SNP-based heritability (GREML), performing mixed linear model association (MLMA/fastGWA), computing genetic relationship ma

GenomicRanges — Bioconductor R package for representing, manipulating, and analyzing genomic intervals (GRanges, GRangesList). Provides operations for finding overlaps (findOverlaps, subsetByOverlaps)

GENOVA — GEnome orgaNizatiOn Visual Analytics, an R package for analysis and visualization of Hi-C and Micro-C chromatin contact data. Provides compartment analysis (A/B compartments, saddle plots), T

GEO Database — NCBI Gene Expression Omnibus public repository for high-throughput gene expression and functional genomics data. Contains 264,000+ series (GSE), 8M+ samples (GSM), 27,000+ platforms (GP

gget — fast CLI and Python interface to 20+ genomic databases. Query gene info (Ensembl), BLAST/BLAT sequences, retrieve AlphaFold structures, perform enrichment analysis (Enrichr), access single-cell

ggplot2 — grammar of graphics implementation in R for creating complex, layered statistical visualizations. Supports scatter plots, bar charts, histograms, boxplots, heatmaps, faceted plots, and custo

Use when working with ggseg — an R package for visualizing brain atlas segmentations using ggplot2 grammar. Creates 2D flat brain maps with ggseg() and 3D interactive visualizations with ggseg3d(). Ac

ggtree — R/Bioconductor package for phylogenetic tree visualization and annotation using ggplot2 grammar. Supports Newick, Nexus, NHX, Jplace, and BEAST tree formats. Enables layer-based annotation wi

Giotto Suite — comprehensive R framework for spatial multi-omics analysis supporting 20+ spatial technologies (Visium, MERFISH, Xenium, CosMx, Slide-seq, seqFISH, CODEX, Stereo-seq). Technology-agnost

Giotto Suite — R toolkit for spatial multi-omics analysis at all scales and resolutions. Processes data from Visium, MERFISH, Xenium, CosMx, Slide-seq, CODEX, Stereo-seq, and other spatial technologie

GLUE (Graph-Linked Unified Embedding) — deep learning framework for integrating unpaired single-cell multi-omics data (scRNA-seq, scATAC-seq, snmC-seq). Uses a guidance graph of prior regulatory inter

gnomAD methods — Broad Institute Python library for working with gnomAD (Genome Aggregation Database) data using Hail. Provides population genetics analysis including variant filtering with VQSR and r

Use when querying or analysing gnomAD (Genome Aggregation Database) variant data: population allele frequencies, variant filtering, constraint scores, loss-of-function intolerance (pLI, LOEUF), struct

GNPS (Global Natural Products Social Molecular Networking) — web-based mass spectrometry platform for molecular networking, spectral library searching, and community-driven metabolomics analysis. Prov

g:Profiler — multi-organism functional enrichment analysis and gene identifier mapping toolkit. Performs over-representation analysis (ORA) against Gene Ontology (GO:BP, GO:MF, GO:CC), KEGG, Reactome,

GraphCast is Google DeepMind's graph neural network for skillful medium-range global weather forecasting. It predicts 10-day forecasts of hundreds of atmospheric variables at 0.25° resolution (~25 km)

Use when working with GraphSAGE — Graph Sample and Aggregate — an inductive graph neural network framework for learning node embeddings on large graphs. Applies to biological network analysis: protein

gt (Grammar of Tables) — R package for creating beautifully formatted, publication-ready display tables from data frames and tibbles. Provides a layered API for headers, spanners, column labels, numer

GTFtools — Python command-line toolkit for parsing, analyzing, and converting GTF/GFF gene annotation files. Extracts gene, transcript, and exon features; computes transcript lengths, exon counts, and

Guppy — Oxford Nanopore Technologies neural-network basecaller for converting raw nanopore signal data (FAST5/POD5) into nucleotide sequences (FASTQ/BAM). Supports GPU-accelerated basecalling, barcodi

GWAS Catalog — EBI/NHGRI curated repository of genome-wide association study summary statistics, significant SNP-trait associations, and ancestry metadata. Query trait-SNP associations, download GWAS

Harmony -- fast and scalable single-cell data integration and batch correction algorithm. Operates on PCA embeddings using iterative soft k-means clustering to remove batch effects while preserving bi

hifiasm — fast haplotype-resolved de novo assembler for PacBio HiFi reads, producing phased telomere-to-telomere genome assemblies. Supports HiFi-only, Hi-C integrated, trio-binning, and ultralong ONT

HistomicsTK — Python toolkit for computational pathology and histopathology image analysis. Provides color normalization and deconvolution of H&E-stained whole-slide images, nuclei segmentation, featu

Human Cell Atlas (HCA) tools — programmatic access to the HCA Data Portal, Data Coordination Platform (DCP), and matrix service for single-cell genomics datasets. Covers the hca Python CLI client, Azu

HUMAnN 3 — functional profiling pipeline for metagenomic and metatranscriptomic shotgun sequencing data. Quantifies gene families (UniRef90/50), metabolic pathways (MetaCyc), and enzyme reactions via

HYSPLIT (Hybrid Single-Particle Lagrangian Integrated Trajectory) is a widely used model for computing air parcel trajectories and simulating the dispersion of pollutants or hazardous materials in the

icclim (Index Calculation for CLIMate) is a Python library for computing standard climate indices from gridded netCDF/xarray climate datasets. It implements the ECA&D and ETCCDI index catalogues and i

IGV (Integrative Genomics Viewer) — high-performance Java desktop application for interactive visualization and exploration of genomic data. Supports BAM/CRAM alignments, VCF variants, BED/GFF annotat

IGV.js — embeddable JavaScript genome browser for interactive visualization of genomic data in web applications. Supports BAM/CRAM alignments, VCF variants, BED annotations, BigWig signal tracks, GFF3

ilastik — interactive machine learning toolkit for bioimage analysis. Provides pixel classification, object classification, autocontext, tracking, counting, carving (3D segmentation), and multicut bou

Use when working with intervaltree — intervaltree — Python mutable interval

InterVar — Python tool for clinical interpretation of genetic variants according to ACMG-AMP 2015 guidelines. Automatically evaluates 28 evidence codes (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) a

IonQuant — high-performance label-free and isobaric (TMT/iTRAQ) quantification engine for mass spectrometry proteomics. Performs MaxLFQ-based protein intensity rollup, match-between-runs (MBR) with 3D

IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,

IsoSeq — PacBio official full-length isoform sequencing pipeline for generating high-quality, full-length cDNA transcripts from PacBio SMRT/HiFi reads. Converts raw CCS reads through primer removal (l

iTOL (Interactive Tree Of Life) — web-based phylogenetic tree display and annotation tool. Visualizes and annotates trees in Newick, Nexus, NHX, and PhyloXML formats. Supports colored nodes/branches,

JBrowse 2 — modern React-based genome browser for interactive visualization of genomic data including BAM/CRAM alignments, VCF variants, BED/GFF annotations, BigWig signal tracks, Hi-C contact maps, a

Jellyfish — fast, multi-threaded k-mer counter for DNA sequences. Counts exact k-mer frequencies in FASTA/FASTQ files using a lock-free hash table. Used for genome size estimation (flow cytometry-free

Joint-Tissue Imputation (JTI) is a unified framework for joint-tissue transcriptome-wide association (TWAS) and Mendelian randomization (MR) analysis. It leverages expression and epigenetic similarity

karyoploteR — R/Bioconductor package for creating publication-quality karyotype plots and genome-wide data visualization along chromosome ideograms. Supports plotting points, lines, bars, links, rainf

KEGG Tools — Kyoto Encyclopedia of Genes and Genomes database access suite for pathway enrichment analysis, gene functional annotation via KEGG Orthology (KO), metabolic pathway reconstruction, and dr

Kipoi — unified Python API and CLI for 2000+ pre-trained machine learning models for genomic sequence analysis. Load, run, and interpret models for variant effect prediction, transcription factor bind

Leafcutter — annotation-free RNA splicing quantification from short-read RNA-seq data. Detects differential intron usage, alternative splicing events, outlier splicing (LeafcutterMD), and splicing QTL

liftOver — UCSC genome coordinate conversion tool for remapping genomic intervals between genome assemblies (e.g., hg19 to hg38, mm10 to mm39). Converts BED, GFF, GTF, VCF, and positional data across

liger (rliger) -- R package for integrative non-negative matrix factorization (iNMF) of single-cell multi-omic data. Integrates scRNA-seq, scATAC-seq, spatial transcriptomics, and methylation datasets