Browse Tools

Chai-1 -- multi-modal foundation model for molecular structure prediction from Chai Discovery. Predicts 3D structures of proteins, nucleic acids (DNA/RNA), small molecules, glycans, ions, and their co

ChEMBL — EMBL-EBI's manually curated database of bioactive molecules with drug-like properties. Query compound bioactivity data, ADMET properties, target annotations, mechanism of action, and approved

ChEMBL Database — manually curated database of bioactive molecules with drug-like properties maintained by EMBL-EBI. Contains 2.4M compounds, 1.6M assays, 20M+ activity measurements, 15K+ targets, and

CHESS (Comparison of Hi-C Experiments using Structural Similarity) — Python command-line tool for quantitative comparison and automatic feature extraction of chromatin contact data using the structura

Use when working with the R package CKMRsim for Close-Kin Mark-Recapture simulation and population size estimation. CKMRsim supports power analysis for CKMR studies, pairwise kinship likelihood ratio

cmocean — perceptually uniform colormaps for oceanographic data visualization. Provides 22 colormaps (thermal, haline, solar, ice, deep, dense, algae, matter, turbid, speed, amp, tempo, rain, phase, t

ColabFold — fast protein structure prediction combining AlphaFold2 with MMseqs2 for rapid MSA generation. Predict monomer and multimer structures, generate multiple sequence alignments, run batch pred

Comet — open-source tandem mass spectrometry (MS/MS) sequence database search engine for peptide identification. Searches MS/MS spectra against FASTA protein databases producing pepXML, mzIdentML, SQT

Conda and Mamba package/environment management for bioinformatics. Create, export, and reproduce isolated software environments using conda or mamba (fast C++ solver). Manage Bioconda channels, resolv

COPASI — COmplex PAthway SImulator for systems biology. Simulates and analyzes biochemical reaction networks using deterministic ODE integration (LSODA, Radau5, CVODE), stochastic simulation (Gibson-B

Use when inferring mechanistic causal links across multiple omics layers with COSMOS (Causal Oriented Search of Multi-Omics Space). Integrates metabolomics, transcriptomics, and signaling pathway data

CPTAC pipelines — Python toolkit for accessing and analyzing Clinical Proteomic Tumor Analysis Consortium (CPTAC) multi-omics cancer data. Provides programmatic download of proteomics, phosphoproteomi

CRISPResso2 — Python tool for quantifying CRISPR genome editing outcomes from amplicon sequencing data. Analyzes NHEJ (insertions, deletions), HDR, and mixed repair outcomes. Supports single amplicon

cryoSPARC — cryo-EM single particle analysis platform for high-resolution 3D structure determination. Provides motion correction, CTF estimation, particle picking (blob, template, Topaz), 2D classific

Cyrius — CYP2D6 star allele genotyping from whole-genome sequencing data. Call CYP2D6 diplotypes (*1/*2, *4/*5) from BAM/CRAM files for pharmacogenomics clinical reporting. Handles CYP2D6/CYP2D7 fusio

DeepChem — Python framework for deep learning in drug discovery, materials science, quantum chemistry, and biology. Provides molecular featurizers (ECFP, graph convolutions, Coulomb matrices), pre-bui

Use when working with dental or oral microbiome analysis — profiling microbial communities from saliva, dental plaque, gingival crevicular fluid, tongue dorsum, or buccal mucosa. Covers 16S rRNA ampli

DepMap/Chronos — Bayesian algorithm for inferring gene fitness effects from CRISPR knockout screen readcount data. Separates true gene knockout effects from copy-number artifacts, guide efficacy varia

Use when working with DGL (Deep Graph Library) — the Python framework for building and training graph neural networks (GNNs). Apply GCN, GAT, GraphSAGE, GIN, and other GNN architectures to biological

DIABLO (Data Integration Analysis for Biomarker discovery using Latent cOmponents) — supervised multi-omics integration method from the mixOmics R package. Performs sparse generalized canonical correl

DiffDock — diffusion generative model for molecular docking that predicts protein-ligand binding poses. Uses a diffusion process over translations, rotations, and torsion angles to generate and rank d

DNABERT — pre-trained BERT model for DNA sequence understanding and classification. Tokenizes DNA using overlapping k-mers (k=3,4,5,6) and provides contextualized embeddings for promoter prediction, s

dnaplotlib — Python library for programmable visualization of genetic designs and synthetic biology circuits. Renders genetic parts (Promoter, RBS, CDS, Terminator, Spacer) as vector-quality matplotli

Dockstore — open platform for sharing Docker-based bioinformatics tools and workflows written in CWL, WDL, Nextflow, and Galaxy. Provides workflow discovery, versioned registrations, TRS API for progr

DoRothEA — Discriminant Regulon Expression Analysis R/Bioconductor package for transcription factor (TF) activity inference from gene expression data. Provides curated TF regulons (confidence levels A

DVC (Data Version Control) — Git-based version control for data, models, and ML experiments. Provides data versioning with .dvc files, ML pipeline definition via dvc.yaml DAGs, experiment tracking and

NVIDIA earth2mip — Earth-2 Model Interoperability Platform for AI weather and climate forecasting. Unified Python framework for running FourCastNet (v1/v2), CorrDiff, and other AI models at 0.25° glob

'Use when working with echtvar — echtvar — ultra-fast Rust CLI for variant

eigenMT — multiple testing correction for QTL mapping using eigenvalue decomposition of the genotype correlation matrix. Estimates the effective number of independent tests (M_eff) per gene for cis-eQ

emmeans — Estimated Marginal Means (least-squares means) in R. Compute marginal means from fitted models with emmeans(), pairwise comparisons with pairs() and contrast(), interaction analysis with joi

EpiDISH — Bioconductor R package for cell-type deconvolution of DNA methylation data. Estimates cell-type proportions from Illumina 450K and EPIC arrays using reference-based methods: Robust Partial C

Evo — genomic foundation model for DNA sequence modeling at single-nucleotide resolution. Uses StripedHyena architecture (7B parameters) trained on 2.7M prokaryotic and phage genomes (OpenGenome datas

EvoDiff — discrete diffusion models for protein sequence generation directly from evolutionary-scale data. Generates novel protein sequences without requiring 3D structures using order-agnostic autore

factoextra — R package for extracting and visualizing multivariate analysis results with ggplot2. Covers PCA (fviz_pca_ind, fviz_pca_var, fviz_pca_biplot), CA (fviz_ca_row, fviz_ca_col, fviz_ca_biplot

WARP (WDL Analysis Research Pipelines) — Broad Institute's cloud-optimized collection of genomics pipelines written in WDL (Workflow Description Language). Covers whole-genome sequencing (WGS), whole-

FPocket — fast open-source protein pocket detection and druggability estimation using Voronoi tessellation and alpha spheres. Identifies binding sites on protein surfaces from PDB structures, scores p

Use when running Transcriptome-Wide Association Studies (TWAS) with FUSION, integrating GWAS summary statistics with precomputed eQTL expression weights to identify genes whose predicted expression is

GA4GH Passport — the Global Alliance for Genomics and Health standard for researcher identity and federated data access authorization. Uses JWT-encoded visa bundles to grant controlled access across i

Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene

NCBI Genome Data Viewer (GDV) — interactive web-based genome browser for exploring RefSeq genome assemblies with gene, variant, and functional annotation tracks. Supports URL-based navigation to speci

Use when working with GenSLMs (Genome-Scale Language Models) for genome sequence generation, embedding, evolutionary analysis, or fine-tuning on viral or bacterial genomes. Covers model loading, infer

GEOfetch — Python tool for downloading and converting GEO and SRA metadata and data into PEP (Portable Encapsulations of Projects) format. Fetches sample metadata from NCBI GEO/SRA, builds standardize

GeoPandas — geospatial vector data analysis in Python. Read/write Shapefile, GeoJSON, GeoPackage, and PostGIS with read_file()/to_file(). Spatial joins with sjoin(), overlay operations (union, interse

Use when working with ggsci, an R package of ggplot2 color palettes inspired by scientific journals, visualization libraries, and science fiction themes. Covers scale_color_*(), scale_fill_*(), and pa

Gnina — deep learning molecular docking program built on AutoDock Vina. Uses convolutional neural networks (CNNs) to rescore protein-ligand poses for improved binding pose prediction and virtual scree

GUIDES (Graphical User Interface for DNA Editing Screens) — web-based tool for designing customized CRISPR-Cas9 guide RNA libraries. Integrates Doench on-target efficiency scoring, tissue-specific gen

Use when performing HLA typing from NGS data with HLA-HD. Covers high-resolution HLA genotyping from WGS, WES, or targeted sequencing FASTQ files, calling classical and non-classical HLA alleles at 3-

HMMRATAC — Hidden Markov Model-based peak caller for ATAC-seq chromatin accessibility data. Identifies nucleosome-free regions (NFR), mono-, di-, and tri-nucleosomal fragments using an HMM that models

IDR (Irreproducible Discovery Rate) — statistical framework for assessing and controlling reproducibility of high-throughput sequencing experiments across biological replicates. Fits a copula mixture

Use when working with imagej — open-source image processing program with