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Bioinformatics Tools

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Bioinformatics software, packages, and analytical pipelines.

Last updated: 2026-07-21

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ALADYNOULLI A Bayesian generative framework that jointly models longitudinal EHR diagnoses, age and polygenic risk to recover latent time-varying disease signatures and patient-specific signature loadings. tool, bayesian, gwas, rvas, machine-learning, statistical-genetics 2026-07-19
AlphaFold 2 A deep-learning system for protein structure prediction from amino-acid sequence and evolutionary information. tool, protein-structure-prediction, deep-learning, computational-biology 2026-07-19
AlphaFold 3 A diffusion-based model for joint structure prediction of proteins, nucleic acids, ligands, ions and modified residues. tool, protein-structure-prediction, deep-learning, computational-biology, drug-discovery 2026-07-19
AlphaGenome A unified DNA sequence model for predicting functional genomic tracks and regulatory variant effects. tool, deep-learning, functional-genomics, genomics, gene-expression 2026-07-19
AUTOENCODIX An open-source, PyTorch-based end-to-end pipeline unifying five autoencoder architectures for standardized, comparable multi-omics representation learning. tool, deep-learning, computational-biology, cancer-genetics, single-cell, transcriptomics 2026-07-20
AutoMorph An automated deep learning pipeline for retinal vascular morphology quantification, image pre-processing, and quality grading. tool, deep-learning, computer-vision, ophthalmology 2026-07-19
BINN An open-source framework for building biologically informed neural networks from Reactome, used to classify clinical proteomic subphenotypes with SHAP-based pathway interpretability. tool, deep-learning, proteomics, bioinformatics, biomarker 2026-07-20
BioPAN A web tool that maps two-condition mammalian lipidomics data onto curated biosynthetic reactions and candidate genes. tool, lipidomics, pathway-analysis, bioinformatics, mass-spectrometry 2026-07-21
CardiOmicScore A multitask deep learning framework that learns disease-specific proteomic and metabolomic risk scores for six cardiovascular diseases from UK Biobank data. tool, cardiovascular-disease, deep-learning, proteomics, metabolomics, polygenic-risk-score, risk-prediction 2026-07-20
CataPro An enzyme kinetic parameter prediction model (kcat, Km, kcat/Km) built on unbiased, sequence-similarity-clustered ten-fold cross-validation datasets, applied to discover and engineer a high-activity vanillin-producing enzyme. tool, enzyme-kinetics, deep-learning, enzyme-engineering, benchmarking 2026-07-20
CatPred A deep learning framework predicting enzyme kcat, Km, and Ki with query-specific uncertainty quantification, evaluated on sequence-identity-stratified out-of-distribution test sets. tool, enzyme-kinetics, deep-learning, uncertainty-quantification, protein-language-model 2026-07-20
Chemosensory Mendelian Randomization Pipeline A bioinformatics pipeline for selecting valid genetic instruments for dietary exposures using taste and olfactory receptor variants. tool, genetics, mendelian-randomization, chemosensory-perception, diet 2026-07-19
DECODE A proteogenomic pipeline for detecting, validating and quantifying amino acid substitutions produced by alternate RNA decoding. tool, pipeline, proteomics, mass-spectrometry, bioinformatics 2026-07-19
DeepMet A chemical language model that anticipates previously unrecognized mammalian metabolites and integrates with mass spectrometry data for de novo metabolite discovery. tool, metabolomics, mass-spectrometry, deep-learning, cheminformatics, structure-elucidation 2026-07-20
DeGAs / dPRS A latent-component decomposition of genome-wide SNP-trait associations used to compute an interpretable, component-resolved polygenic risk score. tool, polygenic-risk-score, gwas, statistical-genetics, disease-subtyping, clustering 2026-07-21
Delphi-2M A modified generative pretrained transformer (GPT-2) architecture designed to model continuous-time human disease progression and multi-disease occurrence trajectories. tool, deep-learning, multi-morbidity 2026-07-19
DLKcat A deep learning model that predicts enzyme turnover numbers (kcat) from protein sequence and substrate structure, used to parameterize enzyme-constrained genome-scale metabolic models at scale; its generalization claims are disputed. tool, enzyme-kinetics, deep-learning, metabolic-modeling 2026-07-20
DreaMS Deep Representations Empowering the Annotation of Mass Spectra, a transformer-based foundation model for mass spectrometry data. tool, mass-spectrometry, foundation-model, transformer 2026-07-20
DrugRepurposing Pipeline An R/Python codebase for benchmarking and performing TWAS-based drug candidate prioritisation using gene expression signature matching. tool, twas, drug-repurposing, gsea, spearman-correlation 2026-07-19
DrugCLIP A contrastive-learning system for rapid protein-pocket and small-molecule retrieval in virtual screening. tool, drug-discovery, deep-learning, cheminformatics, protein-structure-prediction 2026-07-19
Empirical Research Assistance (ERA) An AI system that systematically and automatically creates empirical software to solve scorable tasks. tool 2026-07-20
ENCODE-rE2G A supervised predictive model of enhancer-gene regulatory interactions. tool, statistical-genetics 2026-07-19
EnzGFM An enzyme-specific protein language model using a hierarchically pre-trained Mamba-Transformer hybrid architecture, paired with an agentic pipeline for enzyme mutagenesis and engineering workflows. tool, protein-language-model, enzyme-engineering, deep-learning 2026-07-20
EnzymeTuning A GAN-based top-down framework that globally optimizes kcat values within enzyme-constrained genome-scale metabolic models against in vivo proteomics and growth-phenotype data. tool, enzyme-kinetics, generative-adversarial-network, metabolic-modeling 2026-07-20
ePRS A transfer learning penalization framework that adapts polygenic scores from deeply phenotypically refined cohorts using large-scale GWAS summary statistics. tool, polygenic-risk-score, transfer-learning, genetics 2026-07-19
expiMap A biologically informed deep learning architecture for single-cell reference mapping that encodes query cells into interpretable gene-program latent dimensions. tool, deep-learning, single-cell, computational-biology 2026-07-20
FFRangio A wire-free computational method that estimates fractional flow reserve (FFR) using standard coronary angiography. cardiology, hemodynamics, medical-imaging, machine-learning, computational-simulation 2026-07-19
FIDDLE A deep learning method that predicts molecular formulas directly from tandem mass spectra, outperforming SIRIUS and BUDDY on accuracy and runtime. tool, mass-spectrometry, deep-learning, cheminformatics, structure-elucidation 2026-07-20
FUSION A suite of tools for performing transcriptome-wide and regulome-wide association studies (TWAS and RWAS) using summary statistics. tool, twas, regulome, gene-expression 2026-07-19
flashfmZero An R package for latent-factor GWAS and joint Bayesian fine-mapping of high-dimensional correlated traits. tool, r-package, fine-mapping, multi-trait, statistical-genetics 2026-07-19
Gene-SGAN A multi-view, weakly-supervised deep clustering method that discovers disease subtypes jointly from imaging and genetic data. tool, deep-learning, generative-adversarial-network, medical-imaging, disease-subtyping, clustering, genetics 2026-07-21
Geneformer A transformer-based model for single-cell transcriptomics designed to enable transfer learning in network biology. tool, single-cell, foundation-model, transcriptomics 2026-07-20
Genomic SEM An R package for structural equation modeling of the joint genetic architecture of multiple traits directly from GWAS summary statistics. tool, r-package, gwas, statistical-genetics, polygenic-risk-score, bayesian 2026-07-21
gpu-coloc A GPU-accelerated tool for genetic colocalization analysis across millions of traits. tool, colocalization, statistical-genetics 2026-07-19
GMMAT A generalized linear mixed model association test for GWAS that controls for population structure and relatedness. tool, gwas, statistical-genetics, relatedness 2026-07-21
GWIS A method for approximating GWAS summary statistics for a phenotype defined as a function of other phenotypes. tool, gwas, statistical-genetics, summary-statistics, method 2026-07-20
Heckmann Enzyme Turnover ML Model An early (2018) machine learning model predicting E. coli enzyme turnover numbers from structural, network, and biochemical features, used to improve proteome-allocation genome-scale metabolic models. tool, enzyme-kinetics, machine-learning, metabolic-modeling, protein-structure-prediction 2026-07-20
HyPrColoc An efficient deterministic Bayesian algorithm for multi-trait colocalization using GWAS summary statistics. tool, colocalization, bayesian, multi-trait, gwas 2026-07-19
IWAE Cross-Platform Metabolomics Imputation An ensemble of importance-weighted autoencoders that imputes an entire Metabolon metabolomics dataset from a different platform's features. tool, metabolomics, deep-learning, imputation, statistics 2026-07-20
JointPRS A data-adaptive hierarchical Bayesian framework for multi-population genetic risk prediction incorporating genetic correlation. tool, polygenic-risk-score, multi-ancestry, statistical-genetics 2026-07-19
LIPID Imputation An elastic-net framework for harmonising plasma lipidomic datasets measured at different chromatographic resolutions. tool, lipidomics, lipid-metabolism, imputation, cardiovascular-disease, statistics 2026-07-20
LIPID MAPS An open lipidomics infrastructure providing community standards, curated databases, analysis tools, spectra, pathways, and training. project, lipidomics, bioinformatics, mass-spectrometry, dataset 2026-07-21
LIPID MAPS Lipidomics Tools Guide An interactive decision guide for selecting open, graphical software across the major stages of lipidomics data analysis. tool, lipidomics, bioinformatics, mass-spectrometry, pipeline 2026-07-21
LipiDetective A transformer-based deep learning model that identifies molecular lipid species directly from tandem mass spectra, independent of instrument or experimental setup. tool, lipidomics, mass-spectrometry, transformer, deep-learning, tum 2026-07-21
LipidIN A platform-independent lipidomics annotation framework combining an ultra-fast spectral query engine with a "reverse lipidomics" fingerprint-regeneration network. tool, lipidomics, mass-spectrometry, deep-learning, transformer 2026-07-20
LimeMap A curated, editable pathway map for visualizing omega-3 and omega-6 lipid mediators, related enzymes, receptors, and ion channels. tool, lipidomics, pathway-analysis, inflammation, computational-biology 2026-07-21
McMLP A two-step deep learning method using coupled multilayer perceptrons to predict post-dietary-intervention metabolite concentrations from baseline gut microbiome and metabolome. tool, deep-learning, metabolomics, diet, nutrition 2026-07-20
MendelianRandomization An R package for performing Mendelian randomization analyses using summarized data. tool, r-package, mendelian-randomization 2026-07-19
Multi-scale Erythrocyte Metabolism Platform A structural systems biology workflow (GEM-PRO) integrating protein structures, molecular dynamics, and genome-scale modeling of the human erythrocyte to mechanistically predict how sequence variants alter drug responses. tool, metabolic-modeling, protein-structure-prediction, pharmacogenetics, computational-biology 2026-07-20
MetaboXcan A TWAS-analogous framework that trains genetic predictors of plasma metabolite levels and performs four complementary association analyses to link genetic loci to disease via metabolic mechanisms. tool, metabolomics, twas, statistical-genetics, imputation 2026-07-20
MetaXcan A suite of command-line tools for association mapping of imputed transcriptome and other molecular traits. tool, twas, pwas, association-mapping 2026-07-19
MetDNA3 A two-layer interactive networking platform for untargeted metabolomics that fuses a GNN-expanded metabolic reaction network with a data-driven feature network. tool, metabolomics, mass-spectrometry, deep-learning, cheminformatics 2026-07-20
MetGenX A structure-informed encoder-decoder neural network that generates de novo metabolite structures from MS2 spectra using retrieved template molecules. tool, metabolomics, mass-spectrometry, deep-learning, cheminformatics, structure-elucidation 2026-07-20
MIST Metabolite Inference with Spectrum Transformers, a machine learning tool for molecular structure elucidation from mass spectrometry data. tool, mass-spectrometry, machine-learning, transformer 2026-07-19
MIXPRS A multi-population and multi-method polygenic risk score integration framework that operates solely on GWAS summary statistics. tool, polygenic-risk-score, statistical-genetics, multi-ancestry, data-fission 2026-07-19
Multi-INTACT A Bayesian method that jointly models multiple gene products (e.g., transcript and protein levels) with TWAS and colocalization evidence to implicate causal genes. tool, twas, pwas, colocalization, bayesian, statistical-genetics 2026-07-20
mtVAE A variational autoencoder trained on population-scale blood metabolomics that learns nonlinear, pathway-organized latent representations transferable to unseen disease cohorts. tool, metabolomics, deep-learning, statistics, biomarker 2026-07-20
MultiSuSiE A Python package for multi-ancestry fine-mapping designed for whole-genome sequencing data. tool, fine-mapping, multi-ancestry, wgs 2026-07-19
mvSuSiE An R package for multitrait fine-mapping extending the Sum of Single Effects model. tool, fine-mapping, multitrait 2026-07-19
N-GWAMA / MA-GWAMA Two multivariate GWAS meta-analysis methods that pool summary statistics of genetically correlated traits while correcting for unknown sample overlap. tool, gwas, statistical-genetics, summary-statistics, multi-trait 2026-07-20
NetMoST A network-based machine learning method that clusters patients into disease biotypes from polygenic SNP allele biomarkers. tool, machine-learning, polygenic-risk-score, disease-subtyping, clustering, neuropsychiatric 2026-07-21
OmicsPred A centralised resource for hosting and disseminating genetic prediction models of multi-omic traits. tool, dataset, imputation, transcriptomics, proteomics, metabolomics 2026-07-19
Open Targets A public-private platform for therapeutic target identification and prioritization, integrating genetics, omics, and drug data. tool, drug-discovery, genetics, gwas, variant-to-gene 2026-07-20
OpenGWAS A public database and API for genome-wide association study (GWAS) summary statistics. tool, dataset, gwas, mendelian-randomization 2026-07-19
P-NET A biologically informed, fully-interpretable sparse deep neural network that encodes 3,007 curated pathways to predict prostate cancer disease state from mutation/copy-number data, implicating MDM4 as a therapeutic target. tool, deep-learning, cancer-genetics, oncology, computational-biology 2026-07-20
PanMETAI A TabPFN tabular-foundation-model-based diagnostic algorithm integrating ¹H NMR serum metabolomics with clinical/protein features to detect pancreatic ductal adenocarcinoma. tool, metabolomics, nmr-spectroscopy, machine-learning, oncology, biomarker 2026-07-20
PGS Catalog An open, expertly-curated database of published polygenic scores with full scoring files and standardized metadata, created to address widespread PGS irreproducibility. dataset, polygenic-risk-score, genetics, reference 2026-07-20
PGS Catalog Calculator (pgsc_calc) A reproducible Nextflow pipeline for calculating PGS Catalog scores on individual-level data with genetic-ancestry-aware normalization. tool, polygenic-risk-score, pipeline, nextflow 2026-07-20
PhenomeXcan A gene-based, queryable resource mapping the transcriptome-mediated effects of 8.87 million GWAS variants across 4,091 traits and 22,515 genes, prioritized with the fastENLOC colocalization method. tool, twas, gwas, colocalization, bayesian, dataset 2026-07-20
Pleiotropic Decomposition Regression (PDR) A method that decomposes a SNP's multi-trait effect-size vector into a small number of independent, biologically interpretable pleiotropic components. tool, gwas, statistical-genetics, polygenic-risk-score, pleiotropy 2026-07-21
PLINK A comprehensive open-source C/C++ toolset for whole-genome association and population-based linkage analyses, highly optimized with bit-parallel operations. tool, gwas, statistical-genetics, quality-control 2026-07-19
PredictDB A repository of genetic prediction models of tissue-specific gene expression and splicing. tool, dataset, transcriptomics, gene-expression 2026-07-19
PRSet A pathway-based polygenic risk scoring tool that computes and tests gene-set-restricted PRS instead of a single genome-wide score. tool, polygenic-risk-score, gwas, statistical-genetics, disease-subtyping, clustering 2026-07-21
Protenix An open-source reproduction of AlphaFold 3 for predicting structures of proteins, ligands, nucleic acids and biomolecular complexes. tool, protein-structure-prediction, deep-learning, computational-biology, bioinformatics 2026-07-19
Recon3D The most comprehensive human genome-scale metabolic network reconstruction at publication, integrating 3D metabolite/protein structure data to enable structurally-resolved analysis of metabolic gene variation and drug response. tool, metabolic-modeling, genomics, protein-structure-prediction, computational-biology 2026-07-20
RatXcan A cross-species extension of PrediXcan/TWAS to outbred heterogeneous stock rats, correcting for close familial relatedness and target-trait polygenicity-driven inflation. tool, twas, statistical-genetics, multi-trait, gwas 2026-07-20
REGENIE A highly efficient machine learning method for genome-wide and exome-wide association studies in large cohorts. tool, gwas, statistical-genetics 2026-07-19
Ret-AAE A deep learning framework utilizing retinal adversarial autoencoders to generate low-dimensional representations of CFP and OCT images. tool, deep-learning, computer-vision, ophthalmology, cohort 2026-07-19
RisQ A transformer-based multimodal framework that learns a unified representation of human health across diseases, modalities, and time. tool, multimodal, risk-prediction, deep-learning 2026-07-19
scBERT A large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data. tool, single-cell, foundation-model, transcriptomics 2026-07-20
scPrediXcan A cell-type-specific TWAS framework that trains deep-learning gene-expression predictors (ctPred) from single-cell data, outperforming canonical bulk/pseudobulk TWAS at identifying candidate causal genes. tool, twas, single-cell, deep-learning, statistical-genetics 2026-07-20
Spec2Mol An end-to-end encoder-decoder deep learning architecture that translates MS/MS spectra directly into candidate SMILES molecular structures. tool, mass-spectrometry, metabolomics, deep-learning, cheminformatics, structure-elucidation 2026-07-20
SSimp A method and software for directly imputing GWAS summary statistics at untyped variants from tag-SNV summary statistics and reference-panel LD. tool, gwas, statistical-genetics, summary-statistics, imputation 2026-07-20
scCello A cell-ontology-guided transcriptome foundation model adding cell-type coherence and ontology-alignment losses to pretraining, improving generalization to unseen cell types, tissues, and donors. tool, single-cell, foundation-model, transcriptomics 2026-07-20
scFoundation A large-scale foundation model for single-cell transcriptomics containing 100 million parameters. tool, single-cell, foundation-model, transcriptomics 2026-07-20
scGPT A generative pretrained transformer foundation model for single-cell multi-omics. tool, single-cell, foundation-model, transcriptomics 2026-07-20
SCimilarity An autoencoder-based metric learning framework for cell atlas scale search and annotation. tool, single-cell, foundation-model, transcriptomics 2026-07-19
scVI Single-cell Variational Inference model for deep generative modeling of single-cell transcriptomics. tool, single-cell, transcriptomics, deep-learning 2026-07-19
SDPRX A hierarchical Bayesian cross-population complex trait prediction tool using a Dirichlet process mixture model. tool, polygenic-risk-score, multi-ancestry, statistical-genetics, bayesian 2026-07-19
sMultiXcan An extension of MetaXcan that integrates predicted gene expression across multiple tissues to detect gene-trait associations. tool, twas, multi-tissue, summary-statistics 2026-07-19
SpliceAI A deep learning tool for predicting splice junctions and cryptic splicing from pre-mRNA sequence. tool, statistical-genetics 2026-07-19
sPrediXcan A bioinformatics tool that computes gene-level association summary statistics from GWAS summary statistics and gene expression prediction models. tool, twas, gene-expression, summary-statistics 2026-07-19
Structural Km Predictor A genome-scale, organism-independent Michaelis constant (Km) prediction model combining a graph-neural-network substrate fingerprint with an enzyme-sequence representation. tool, enzyme-kinetics, machine-learning, metabolic-modeling 2026-07-20
SuShiE A Python package for multiancestry fine-mapping of molecular phenotypes using JAX. tool, fine-mapping, multi-ancestry, jax 2026-07-19
SuSiEx A command-line tool for cross-population genetic fine-mapping. tool, fine-mapping, multi-ancestry 2026-07-19
Tractor A local-ancestry-informed generalized linear model for GWAS in admixed cohorts, producing ancestry-specific effect sizes. tool, gwas, statistical-genetics, admixture, local-ancestry, multi-ancestry 2026-07-21
Tractor-Mix A local-ancestry-informed generalized linear mixed model enabling well-calibrated GWAS in admixed cohorts with sample relatedness. tool, gwas, statistical-genetics, admixture, local-ancestry, relatedness, multi-ancestry, r-package 2026-07-21
TranscriptFormer A generative, autoregressive single-cell foundation model trained on 112 million cells across 12 species spanning 1.53 billion years of evolution, outperforming UCE on evolutionarily distant cross-species tasks. tool, single-cell, foundation-model, transcriptomics, protein-language-model 2026-07-20
TurNuP An organism-independent turnover number (kcat) prediction model combining differential reaction fingerprints with a retrained protein Transformer, designed to generalize to enzymes dissimilar from its training set. tool, enzyme-kinetics, machine-learning, metabolic-modeling 2026-07-20
TwoSampleMR An R package for performing two-sample Mendelian randomization analyses using GWAS summary data. tool, r-package, mendelian-randomization 2026-07-19
UCE (Universal Cell Embedding) A 650M-parameter zero-shot foundation model mapping any cell from any tissue/species into a shared embedding space via ESM2 protein-embedding gene tokenization. tool, single-cell, foundation-model, transcriptomics, protein-language-model 2026-07-20
UniKP A unified pretrained-language-model framework predicting enzyme kcat, Km, and kcat/Km from protein sequence and substrate structure, with an environmental-factor extension (EF-UniKP). tool, enzyme-kinetics, machine-learning, protein-language-model 2026-07-20
WikiPathways An open, community-curated pathway database that provides machine-readable biological pathways for visualization and multi-omic analysis. tool, bioinformatics, pathway-analysis, metabolomics, lipidomics 2026-07-21

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