This is an automatically generated1 ranked list of open source software from pharmaceutical companies and cross organizations, biotechnology companies, research institutes, open source communities and individuals, plus some life-science software from technological companies.
It's made from a curated list of GitHub accounts, and will be periodically refreshed from these sources' repositories.
You can also access what they have updated lately and which topics are covered by these software.
Note
stars - number of people who especially appreciated the repository
forks - number of people who have cloned the repository in order to modify it
watchers - number of people who are monitoring changes in the repository
main programming language
license
last update date & time
| Rank | Software |
|---|---|
| 163 | AstraZeneca/awesome-drug-pair-scoring Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022) chemistry, ddi, decagon, deep-chemistry, deep-learning, drug, drug-combination, drug-design, drug-drug-interaction, drug-repurposing, drug-synergy, drug-target-interactions, gcn, gnn, graph-neural-network, knowledge-graph, machine-learning, polypharmacy, relational-learning, synergy-prediction 86 14 Apache License 2.0 2022-08-07 17:10:49 |
| 163 | bioinform/rnacocktailrna-seq 86 48 Jupyter Notebook Other 2020-11-11 06:42:10 |
| 164 | lh3/unimap A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment bioinformatics, genomics, sequence-alignment 85 4 C MIT License 2021-04-08 03:36:36 |
| 165 | Bioconductor/GenomicDataCommons Provide R access to the NCI Genomic Data Commons portal. api-client, bioconductor, bioinformatics, cancer, core-services, data-science, genomics, nci, r, tcga, vignette 82 23 R 2024-05-15 21:04:37 |
| 165 | EliLillyCo/LillyMol LillyMol Public Code 82 29 C++ Apache License 2.0 2024-03-15 21:39:57 |
| 165 | deepchem/moleculenet Moleculenet.ai Datasets And Splits 82 19 Jupyter Notebook MIT License 2021-04-29 19:51:06 |
| 166 | Novartis/YADA Open-source Data Ops 81 21 Java Apache License 2.0 2022-11-16 09:27:33 |
| 166 | lh3/srf SRF: Satellite Repeat Finder 81 5 TeX MIT License 2024-01-08 21:03:02 |
| 167 | aws-samples/aws-healthcare-lifescience-ai-ml-sample-notebooks 80 34 9 Jupyter Notebook MIT-0 license |
| 168 | lh3/minipileup Simple pileup-based variant caller bioinformatics, variant-calling 79 5 C 2024-03-31 22:57:48 |
| 169 | AstraZeneca/biology-for-ai learning biology syllabus, geared for machine learning folks 78 10 2022-12-05 16:29:03 |
| 169 | AstraZeneca-NGS/reference_data Reference data: BED files, genes, transcripts, variations. 78 28 Python 2017-11-28 14:42:42 |
| 169 | bioinform/varsim VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications genomics, high-throughput-sequencing, simulation, validation 78 31 Java BSD 2-Clause "Simplified" License 2023-04-07 01:32:48 |
| 169 | Exscientia/molflux A foundational package for molecular predictive modelling 78 9 Python MIT License 2024-06-03 14:19:51 |
| 170 | Bayer-Group/tiffslide TiffSlide - cloud native openslide-python replacement based on tifffile digital-pathology, python 77 11 Python Other 2024-02-14 16:52:45 |
| 170 | calico/solo software to detect doublets 77 13 Python MIT License 2024-05-03 22:11:11 |
| 170 | microsoft/BioModelAnalyzer BioModelAnalyzer is a user-friendly tool for constructing biological models and verifying them 77 22 14 C specific |
| 171 | Merck/r2rtf Easily Create Production-Ready Rich Text Format (RTF) Table and Figure 76 19 R GNU General Public License v3.0 2024-06-03 01:28:44 |
| 171 | flaxsearch/BioSolr A project aiming "to significantly advance the state of the art with regard to indexing and querying biomedical data with freely available open source software" 76 26 24 Java Apache-2.0 license |
| 172 | deepchem/jaxchem JAXChem is a JAX-based deep learning library for complex and versatile chemical modeling 74 9 Python 2020-07-15 05:02:21 |
| 172 | lh3/fermi A WGS de novo assembler based on the FMD-index for large genomes bioinformatics, denovo-assembly, genomics 74 15 C 2013-12-06 16:46:42 |
| 173 | calico/scnym Semi-supervised adversarial neural networks for classification of single cell transcriptomics data adversarial-training, rna-seq, semi-supervised, single-cell, single-cell-genomics 73 12 Python Apache License 2.0 2023-12-11 23:31:02 |
| 173 | DeepGraphLearning/ProtST [ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts 73 8 4 Python Apache-2.0 license |
| 174 | Bioconductor/BiocWorkshops 72 53 TeX 2019-05-15 21:49:48 |
| 174 | Bayer-Group/ol-kit Easy to use, open source React/Openlayers geospatial component toolkit. bayer, components, deprecated, geospatial, maps, openlayers, react, toolkit 72 19 JavaScript Other 2022-12-07 20:44:37 |
| 174 | genentech/scimilarity A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training. 72 1 Python Other 2024-03-22 23:43:02 |
| 174 | lh3/fermi-lite Standalone C library for assembling Illumina short reads in small regions bioinformatics, denovo-assembly, genomics 72 23 C MIT License 2022-12-15 19:15:52 |
| 174 | shenwei356/unikmer A versatile toolkit for k-mers with taxonomic information difference, golang, intersection, k-mer, kmer, set, unik, union, unique 72 7 3 Go MIT license 2024-06-08 10:10:28 |
| 175 | Bioconductor/bioconductor_docker Docker Containers for Bioconductor - NEW! bioconductor, bioconductor-containers, docker-image 71 30 Shell Artistic License 2.0 2024-06-07 18:03:43 |
| 175 | AstraZeneca/jazzy Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules. 71 6 Python Other 2024-06-06 23:28:22 |
| 175 | insightsengineering/tern Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials clinical-trials, graphs, listings, nest, outputs, r, tables 71 17 R Other 2024-06-04 22:41:07 |
| 175 | lh3/dna-nn Model and predict short DNA sequence features with neural networks bioinformatics, deep-learning, genomics 71 10 C 2019-06-16 01:49:30 |
| 175 | bigdatagenomics/avocado A Variant Caller, Distributed. Apache 2 licensed. 71 42 Scala Apache License 2.0 2019-03-11 21:33:58 |
| 175 | scverse/scanpy_usage Scanpy use cases. 71 59 HTML BSD 3-Clause "New" or "Revised" License 2020-09-04 07:26:10 |
| 176 | Bioconductor/BiocManager CRAN Package For Managing Bioconductor Packages core-services, cran, r-package 69 22 R 2024-05-10 20:59:33 |
| 176 | Bioconductor/LearnBioconductor Training material for introductory R / Bioconductor courses 69 33 R 2023-03-15 20:25:16 |
| 176 | owkin/GrAIdient GrAIdient is a deep learning framework that aims at challenging the way we train and run models in computer vision. bu--dept-diagnostics-tools, environment--development, owner--jeanfrancoisreboud 69 2 Swift MIT License 2024-06-06 15:52:23 |
| 177 | genentech/pviz Pviz 68 22 JavaScript Other 2016-09-13 06:28:27 |
| 177 | lh3/ropebwt2 Incremental construction of FM-index for DNA sequences bioinformatics, fm-index 68 5 TeX MIT License 2021-02-01 20:48:00 |
| 177 | lh3/bfc High-performance error correction for Illumina resequencing data bioinformatics, genomics 68 13 TeX MIT License 2016-05-31 20:24:20 |
| 177 | scverse/mudata Multimodal Data (.h5mu) implementation for Python anndata, data-analysis, genomics, mudata, multi-omics, multimodal-omics-analysis, muon, scverse 68 16 Python BSD 3-Clause "New" or "Revised" License 2023-10-03 17:09:28 |
| 178 | pharmaverse/ggsurvfit 67 19 R Other 2024-05-17 17:35:21 |
| 178 | MolecularAI/pysmilesutils Utilities for working with SMILES based encodings of molecules for deep learning (PyTorch oriented) 67 18 Python Apache License 2.0 2024-05-23 09:54:27 |
| 178 | Novartis/peax Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders autoencoder, data-visualization, deep-learning, epigenomics, interactive-machine-learning, pattern-search, sequential-data 67 14 Jupyter Notebook Other 2022-12-14 18:38:58 |
| 178 | aqlaboratory/hsm Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning." 67 22 Jupyter Notebook MIT License 2024-04-26 18:13:25 |
| 178 | neurogenomics/MAGMA_Celltyping Find causal cell-types underlying complex trait genetics genomics, gwas, magma, single-cell, single-cell-omics, snps, statistical-genetics 67 29 R 2024-05-17 16:58:37 |
| 178 | DeepGraphLearning/DiffPack Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing deep-learning, diffusion-models, molecule, protein-structure, score-based-generative-modeling, score-matching 67 5 8 Python MIT license |
| 179 | MolecularAI/PaRoutes Home of the PaRoutes framework for benchmarking multi-step retrosynthesis predictions. 66 5 Python Apache License 2.0 2022-11-23 14:27:04 |
| 179 | calico/borzoi RNA-seq prediction with deep convolutional neural networks. 66 6 Python Apache License 2.0 2024-05-27 00:45:13 |
| 179 | neurogenomics/MungeSumstats Rapid standardisation and quality control of GWAS or QTL summary statistics bioconductor-package, bioinformatics, database-api, genomics, gwas, qtl, r, r-package, standardisation, summary-statistics, vcf-files 66 15 R 2024-05-02 07:23:53 |
| 179 | neurogenomics/rworkflows Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳. bioconductor, containers, continuous-integration, cran-r, docker, dockerhub, github-actions, r, reproducibility, workflows 66 6 HTML 2024-02-01 11:09:45 |
| 179 | scverse/cookiecutter-scverse Cookiecutter template for scverse 66 8 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 12:59:20 |
| 180 | Bioconductor/OrchestratingSingleCellAnalysis Content for the OSCA Book. book, book-base, rna-seq, single-cell, single-cell-rna-seq 64 37 Dockerfile 2023-03-15 21:05:28 |
| 180 | OpenGene/OpenGene.jl (No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia bioinformatics, julia, ngs 64 15 Julia Other 2022-07-18 01:42:12 |
| 181 | Bioconductor/BiocParallel Bioconductor facilities for parallel evaluation bioconductor-package, core-package 63 29 R 2024-05-01 16:24:31 |
| 181 | GSK-Biostatistics/tfrmt r package for formatting tables 63 3 R Other 2024-04-16 12:52:10 |
| 181 | Merck/DeepNeuralNet-QSAR 63 27 Python GNU General Public License v3.0 2018-10-24 20:07:27 |
| 181 | OpenBioSim/biosimspace An interoperable Python framework for biomolecular simulation. biomolecular-simulation, computational-biology, computational-chemistry, computational-physics, drug-discovery, free-energy-calculations, interoperability, molecular-dynamics, molecular-simulation, reproducibility, reproducible-research 63 10 Python GNU General Public License v3.0 2024-06-06 15:50:31 |
| 181 | greenelab/BioBombe BioBombe: Sequentially compressed gene expression features enhances biological signatures autoencoder, biobombe, compression, gene-expression, gene-sets, hetnet, msigdb, network, tcga 63 23 6 Jupyter Notebook BSD-3-Clause license 2020-04-08 16:57:32 |
| 182 | AstraZeneca/KAZU Fast, world class biomedical NER biomedical-text-mining, natural-language-processing, nlp 61 4 Python Apache License 2.0 2024-06-04 16:07:59 |
| 182 | aqlaboratory/genie2 Protein structure diffusion model for unconditional protein generation and motif scaffolding 61 7 Python Apache License 2.0 2024-06-03 20:59:28 |
| 182 | EBISPOT/DUO Ontology for consent codes and data use requirements biomedical-applications, biomedical-informatics, datasets-tagged, genomics-data, obofoundry, ontology, owl 61 15 Makefile Other 2022-09-21 14:41:14 |
| 183 | deepchem/deepchem-gui A simple web GUI for DeepChem 59 19 JavaScript MIT License 2023-11-27 17:26:15 |
| 183 | lh3/tabtk Toolkit for processing TAB-delimited format 59 12 C 2016-09-08 13:57:23 |
| 183 | xfengnefx/hifiasm-meta (forked from: chhylp123/hifiasm) hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 59 8 5 C++ MIT license 2023-01-26 22:03:59 |
| 184 | molecularinformatics/Computational-ADME 58 13 Python MIT License 2024-02-15 15:20:55 |
| 184 | OpenGene/CfdnaPattern Pattern Recognition for Cell-free DNA bioinformatics, cfdna, ngs, pattern 58 21 Python MIT License 2018-08-03 03:40:52 |
| 185 | pfizer-opensource/scikit-digital-health Python package for the processing and analysis of Inertial Measurement Unit Data actigraphy, imu-sensor, python, sensors, wearables 57 19 Python MIT License 2024-06-07 16:22:37 |
| 186 | AstraZeneca/kallisto Efficiently calculate 3D-features for quantitative structure-activity relationship approaches. chemistry, computational-chemistry, machinelearning, quantum-chemistry 56 21 Python Apache License 2.0 2024-02-01 10:34:54 |
| 186 | AstraZeneca/judgyprophet Forecasting for knowable future events using Bayesian informative priors (forecasting with judgmental-adjustment). ai, bayesian, data-science, forecasting, machine-learning, python, statistics 56 2 Python Apache License 2.0 2022-04-14 09:16:16 |
| 186 | MolecularAI/reaction_utils Utilities for working with datasets of chemical reactions, reaction templates and template extraction. 56 7 Python Apache License 2.0 2024-05-27 11:35:22 |
| 186 | chembl/mychembl Resources used to create the myChEMBL virtual machine 56 29 Jupyter Notebook 2017-03-20 16:34:46 |
| 186 | DeepGraphLearning/ESM-GearNet ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275) 56 9 3 Python |
| 187 | insightsengineering/thevalidatoR Github Action that generates R Package Validation documentation 🏁 github-actions, r, r-package-automation, validation 54 5 R MIT License 2024-06-03 10:45:44 |
| 187 | EBISPOT/efo Github repo for the Experimental Factor Ontology (EFO) 54 14 Makefile 2024-06-07 11:24:56 |
| 187 | lh3/gwfa Proof-of-concept implementation of GWFA for sequence-to-graph alignment 54 C MIT License 2024-05-29 01:38:18 |
| 188 | MolecularAI/Icolos Icolos: A workflow manager for structure based post-processing of de novo generated small molecules 53 14 Python Apache License 2.0 2023-03-16 16:16:25 |
| 188 | Bayer-Group/goldengate-kafka-adapter An adapter for Oracle GoldenGate to push change capture data directly to an Apache Kafka cluster 53 15 Java Other 2015-10-26 19:08:32 |
| 188 | rdkit/django-rdkit 53 26 Python BSD 3-Clause "New" or "Revised" License 2024-04-29 21:54:50 |
| 188 | bioinform/metasv MetaSV: An accurate and integrative structural-variant caller for next generation sequencing 53 22 Python BSD 2-Clause "Simplified" License 2017-06-30 00:32:20 |
| 189 | Novartis/cellxgene-gateway Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets. dataviz, h5ad, rna-seq, scientific, scrna-seq, transcriptomics, visualization 52 32 Python Apache License 2.0 2024-03-10 13:36:17 |
| 189 | lh3/htsbox (forked from: samtools/htslib) My experimental tools on top of htslib. NOT OFFICIAL!!! bioinformatics, genomics, sequence-analysis 52 7 C Other 2023-08-16 01:54:46 |
| 189 | aws-samples/amazon-omics-tutorials 52 21 9 Python Apache-2.0 license |
| 190 | phuse-org/valtools Validation framework for R packages used in clinical research and drug development. 51 10 R Other 2024-03-08 00:18:18 |
| 190 | MolecularAI/QSARtuna QSARtuna: QSAR model building with the optuna framework compchem, computational-chemistry, hyperparameter-optimization, optuna, qsar, qsar-models, smiles-strings 51 10 Jupyter Notebook 2024-04-24 08:47:24 |
| 190 | MolecularAI/Lib-INVENT 51 30 Jupyter Notebook Apache License 2.0 2023-03-11 11:39:46 |
| 190 | Merck/matcher Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over searching structure/activity relationships (SAR) derived from large datasets, and takes the form of an accessible web application with simple deployment. Matcher is built around the mmpdb platform. chemistry, docker-compose, drug-discovery, search-algorithm, search-engine, web-application 51 9 Python MIT License 2024-02-21 15:13:53 |
| 190 | rdkit/UGM_2020 Materials from the (virtual) 2020 RDKit UGM 51 22 Jupyter Notebook 2020-10-26 03:39:26 |
| 190 | genentech/sVAE 51 5 Python Apache License 2.0 2023-07-21 14:07:07 |
| 190 | insilicomedicine/BiAAE Molecular Generation for Desired Transcriptome Changes with Adversarial Autoencoders 51 15 Python MIT License 2020-07-17 13:56:04 |
| 190 | soedinglab/MMseqs2-App MMseqs2 app to run on your workstation or servers alphafold2, bioinformatics, colabfold, docker, docker-compose, electron, foldseek, golang, mmseqs, profile-search, sequence-search, structure-search, vue 51 16 Vue GNU General Public License v3.0 2024-05-22 08:26:10 |
| 191 | Boehringer-Ingelheim/pyPept pyPept: a python library to generate atomistic 2D and 3D representations of peptides 50 9 Python MIT License 2024-04-30 17:12:07 |
| 192 | Bioconductor/bioc_docker [DEPRECATED] Docker containers for Bioconductor bioconductor-dockers 49 27 R Artistic License 2.0 2023-03-15 20:25:37 |
| 192 | Bayer-Group/stax AWS CloudFormation stack manager 49 8 Shell Other 2015-08-31 18:03:41 |
| 192 | rdkit/conda-rdkit Conda build recipe for the rdkit 49 30 C 2022-01-11 05:44:22 |
| 192 | lh3/CHM-evalbioinformatics, genomics, variant-calling 49 8 TeX MIT License 2020-06-24 15:25:22 |
| 192 | soedinglab/WIsH Predict prokaryotic host for phage metagenomic sequences 49 9 C++ GNU General Public License v3.0 2021-04-08 08:56:53 |
| 193 | Bioconductor/Biostrings Efficient manipulation of biological strings bioconductor-package, core-package 48 16 R 2024-06-07 17:02:36 |
| 193 | Roche/gitlab-configuration-as-code Manage GitLab configuration as code to make GitLab easily managable, traceable and reproducible. configuration-as-code, configuration-management, gitlab, gitlab-api, yaml 48 5 Python Apache License 2.0 2022-08-01 12:18:52 |
| 193 | lh3/miniwfa A reimplementation of the WaveFront Alignment algorithm at low memory bioinformatics, sequence-alignment 48 3 C MIT License 2024-05-22 19:36:07 |
| 194 | EliLillyCo/pytest-wdl WDL plugin for pytest 47 8 Python Apache License 2.0 2023-08-01 23:14:28 |
| 194 | genentech/walk-jump Official repository for discrete Walk-Jump Sampling (dWJS) antibody, machine-learning, protein-design, protein-sequences, proteins 47 8 Python Apache License 2.0 2023-12-17 18:15:08 |
| 194 | insilicomedicine/fcd_torch Fréchet ChemNet Distance on PyTorch 47 14 Python MIT License 2019-03-22 16:25:40 |
| 194 | chembl/chembl_beaker RDKit wrapper 47 23 Python Other 2024-04-09 06:53:28 |
| 195 | Merck/rdf2x RDF2X converts big RDF datasets to the relational database model, CSV, JSON and ElasticSearch. conversion, json, linked-data, postgresql, rdf, spark, sparql, sql 46 11 Java Apache License 2.0 2024-04-15 12:37:25 |
| 195 | bedapub/besca BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis 46 16 Python GNU General Public License v3.0 2024-04-03 15:30:42 |
| 195 | ebi-uniprot/ProtVista A BioJS viewer for protein sequence features 46 18 JavaScript Apache License 2.0 2022-12-02 02:24:18 |
| 195 | lh3/jstreeview Interactive phylogenetic tree viewer/editor bioinformatics, phylogenetics 46 3 JavaScript 2023-07-12 20:16:30 |
| 195 | lh3/samtools This is NOT the official repository of samtools. 46 39 C MIT License 2017-06-09 14:02:16 |
| 195 | shenwei356/ClipboardTextJoiner Monitoring system clipboard change and joining multi-line text. It's very useful when copying multi-line text from PDF files. 46 10 Perl MIT License 2016-07-22 12:52:03 |
| 196 | Bayer-Group/column-resizer Adds resizable columns to tables 45 23 JavaScript Other 2023-10-26 02:34:31 |
| 196 | healx/lig3dlens 45 2 Python MIT License 2024-05-30 15:19:41 |
| 196 | recursionpharma/rxrx1-utils Starter code for the CellSignal NeurIPS 2019 competition. 45 27 Jupyter Notebook Apache License 2.0 2023-03-24 23:08:28 |
| 197 | Bioconductor/BiocIntro Course material for introductory R / Bioconductor courses 44 46 2023-03-15 20:27:19 |
| 197 | AstraZeneca/skywalkR code for Gogleva et al manuscript drug-discovery, knowledge-graph, recommender-system, shiny-apps, ui 44 15 R Apache License 2.0 2022-11-30 11:08:58 |
| 197 | Bayer-Group/stoop Monadic Scala API for CouchDB beat-not-applicable 44 4 Scala Other 2015-01-13 17:13:53 |
| 197 | Novartis/scar scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics cite-seq, crispr-screen, denoising-algorithm, generative-model, machine-learning, probabilistic-graphical-models, pytorch, single-cell-rna-seq, variational-autoencoder 44 4 Python 2024-05-28 21:20:32 |
| 197 | rdkit/homebrew-rdkit Homebrew formula for rdkit 44 19 Ruby 2022-06-22 08:12:35 |
| 197 | lh3/etrf Exact Tandem Repeat Finder (not a TRF replacement) bioinformatics 44 2 C 2019-10-22 14:37:19 |
| 198 | Bayer-Group/COLID-Documentation The documentation repository is part of the Corporate Linked Data Catalog - short: COLID - application. cloud-native, colid, data-catalog, data-catalogue, elasticsearch, fair, fair-data, findable, linked-data, rdf, shacl, triplestore 43 6 HTML BSD 3-Clause "New" or "Revised" License 2023-02-10 16:19:23 |
| 198 | owkin/DSB2017 Data Science Bowl 2017 : Lung Cancer Detection 43 15 Python 2017-05-09 14:40:16 |
| 198 | aws-samples/aws-healthimaging-samples Sample projects on working with AWS HealthImaging, an AWS service that allows you to store, analyze, and share medical images in the cloud at petabyte scale. 43 77 4 JavaScript MIT-0 license |
| 199 | Bioconductor/GoogleGenomics An R package for Google Genomics API queries. bioconductor-packages, core-package, retired-package 42 26 R Apache License 2.0 2023-03-15 20:25:05 |
| 199 | rdkit/UGM_2022 Materials from the 2022 UGM 42 14 Jupyter Notebook 2022-10-31 16:30:51 |
| 199 | chembl/GLaDOS Web Interface for ChEMBL @ EMBL-EBI chembl, cheminformatics, chemistry, chemoinformatics, drug-discovery, drug-targets, molecular-structures, webapp 42 5 JavaScript Other 2022-04-22 20:51:42 |
| 199 | ome/apacheds-docker (forked from: FlechaRoja/ApacheDS) Dockerfile to build an ApacheDS container providing an LDAP and optionally a Kerberos service. docker, ldap, ome, testing 42 60 8 Python 2024-03-22 19:26:03 |
| 199 | soedinglab/spacedust Discovery of conserved gene clusters in multiple genomes 42 1 C GNU General Public License v3.0 2023-08-17 12:52:30 |
| 199 | OpenGene/UniqueKMER Generate unique KMERs for every contig in a FASTA file bioinformatics, fasta, kmer, ngs, sequencing, unique, virus 42 8 C MIT License 2022-08-17 10:38:24 |
| 200 | Bioconductor/GenomicRanges Representation and manipulation of genomic intervals bioconductor-package, core-package 41 17 R 2024-04-30 18:34:53 |
| 200 | MolecularAI/MolBART Pretrained SMILES transformation model for finetuning for diverse molecular tasks. 41 9 Python Apache License 2.0 2022-02-22 19:17:46 |
| 200 | insitro/ChannelViT Channel Vision Transformers: An Image Is Worth C x 16 x 16 Words computer-vision, machine-learning, vision-transformer 41 3 Python Other 2024-02-22 01:08:41 |
| 200 | Path-AI/hif2gene Data and code to accompany our Nature publication deep-learning, pathology 41 13 Jupyter Notebook Other 2022-05-03 16:38:38 |
| 200 | lh3/ref-gen Human reference genome analysis sets 41 2 Makefile 2023-06-17 04:28:15 |
| 200 | scverse/pytometry Flow & mass cytometry analytics. 41 10 Python Apache License 2.0 2024-06-04 09:18:39 |
| 200 | shenwei356/gtdb-taxdump GTDB taxonomy taxdump files with trackable TaxIds bioinformatics, gtdb, taxdump, taxid, taxonkit, taxonomy 41 2 R MIT License 2024-04-24 07:25:00 |
| 201 | Bayer-Group/xsmiles Visualize atom and non-atom attributions and SMILES strings 40 4 TypeScript BSD 3-Clause "New" or "Revised" License 2023-07-12 06:10:57 |
| 201 | johnsonandjohnson/Guppy-iOS iOS pod about a curious fish named Guppy guppy, ios, network-monitoring, networking, swift, urlsession 40 3 Swift Apache License 2.0 2022-02-03 20:25:07 |
| 201 | Merck/Sapiens Sapiens is a human antibody language model based on BERT. antibody, bert, embeddings, language-model, sapiens 40 13 Jupyter Notebook MIT License 2023-04-19 13:14:46 |
| 201 | rdkit/UGM_2021 Materials from the (virtual) 2021 RDKit UGM 40 18 Jupyter Notebook 2021-10-22 11:44:33 |
| 201 | Exscientia/physicsml A package for all physics based/related models 40 1 Python MIT License 2024-06-04 11:25:20 |
| 201 | microsoft/zero-shot-scfoundation 40 6 7 Jupyter Notebook MIT license |
| 201 | scverse/scvi-tutorials Notebooks used in scvi-tools tutorials scverse, scvi-tools, tutorial 40 24 Jupyter Notebook BSD 3-Clause "New" or "Revised" License 2024-06-03 21:37:34 |
| 202 | pharmaverse/logrx Tools to facilitate logging in a clinical environment with the goal of making code easily traceable and reproducible. 39 6 HTML Other 2024-04-12 16:25:31 |
| 202 | Novartis/shinyValidator Audit your Shiny apps at each commit. Multiple levels of testings are offered: startup and crash tests, performance tests (load test and global code profiling), reactivity audit as well as output tests. All results are gathered in an HTML report uploaded and available to everyone on any CI/CD plaform or RStudio Connect audit, headless, profiling, r, shiny, shinyloadtest, shinytest2 39 3 HTML Other 2023-08-10 10:49:42 |
| 202 | Roche/foxops Templating for Git Repositories 39 6 Python Apache License 2.0 2024-05-27 19:22:11 |
| 202 | schrodinger/coordgenlibs Schrodinger-developed 2D Coordinate Generation 39 28 C++ BSD 3-Clause "New" or "Revised" License 2023-11-27 19:57:11 |
| 202 | neurogenomics/orthogene 🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️ animal-models, bioconductor, bioconductor-package, bioinformatics, biomedicine, comparative-genomics, evolutionary-biology, genes, genomics, ontologies, r, r-package, translational-research 39 4 R 2023-12-22 05:46:07 |
| 202 | bigdatagenomics/bdg-formats Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed. 39 36 Shell Apache License 2.0 2024-01-03 19:34:28 |
| 202 | OBF/obf-docs Official documents of the Open Bioinformatics Foundation 39 20 HTML 2023-12-19 22:03:54 |
| 202 | chao1224/GeoSSL GeoSSL: Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching, ICLR'23 (https://openreview.net/forum?id=CjTHVo1dvR) denoising-diffusion, diffusion-models, geometry, molecular-geometries, molecule, pretraining, self-supervised, self-supervised-learning 39 1 2 Python MIT license 2023-07-27 11:22:53 |
| 203 | AstraZeneca/runnable Runnable 38 4 Python Apache License 2.0 2024-06-04 20:42:58 |
| 203 | Bayer-Group/kamon-prometheus A Kamon backend to support Prometheus 38 19 HTML Other 2017-06-22 19:33:30 |
| 203 | bigdatagenomics/cannoli Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed. 38 17 Scala Apache License 2.0 2024-04-24 19:17:12 |
| 204 | pharmaverse/falcon FDA Safety Tables and Figures 37 5 R Other 2024-05-30 22:46:19 |
| 204 | rdkit/shape-it Updated version of Silicos-it's shape-based alignment tool 37 11 C++ MIT License 2024-03-23 04:22:24 |
| 204 | biosustain/shu Multi-dimensional, trans-omics metabolic maps. metabolism, systems-biology, visualization 37 Rust Apache License 2.0 2024-03-18 13:59:48 |
| 204 | lh3/bioseq-js For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml bioinformatics, sequence-alignment 37 13 HTML Other 2019-08-08 20:16:54 |
| 204 | scverse/anndataR AnnData interoperability in R anndata, h5ad 37 6 R Other 2024-04-23 13:43:35 |
| 204 | chao1224/n_gram_graph N-Gram Graph: Simple Unsupervised Representation for Graphs, NeurIPS'19 (https://arxiv.org/abs/1806.09206) drug, drug-discovery, molecular-graph, molecule, n-gram, n-gram-graph, pretraining 37 8 3 Python MIT license 2021-04-14 15:17:12 |
| 205 | novonordisk-research/ProcessOptimizer A tool to optimize real world problems bayesianoptimization, optimization 36 12 Jupyter Notebook Other 2024-05-07 11:21:24 |
| 205 | OpenBioSim/sire Sire Molecular Simulations Framework biomolecular-simulation, cplusplus, free-energy-calculations, molecular-simulation, python 36 7 C++ GNU General Public License v3.0 2024-06-03 18:25:50 |
| 205 | ebi-gene-expression-group/anatomogram Anatomogram illustrating Expression Atlas experiments anatomy, react, svg 36 20 JavaScript 2020-07-30 09:30:02 |
| 205 | OpenGene/ctdna-pipeline A simplified pipeline for ctDNA sequencing data analysis bioinformatics, ctdna, liquid-biopsy, ngs, pipeline 36 16 Shell MIT License 2017-09-23 05:32:49 |
| 206 | Bioconductor/OrchestratingSingleCellAnalysis-release An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis. book, book-release, rna-seq, single-cell, single-cell-rna-seq 35 8 2023-03-15 21:04:51 |
| 206 | Novartis/torchsurv Deep survival analysis made easy deep-learning, pytorch, survival-analysis 35 5 Python MIT License 2024-04-29 18:57:39 |
| 206 | Novartis/ontobrowser OntoBrowser is a web-based application for managing ontologies 35 9 Java Apache License 2.0 2023-02-15 10:40:14 |
| 206 | rdkit/UGM_2016 Materials from the 2016 RDKit UGM 35 21 Jupyter Notebook 2017-01-09 08:40:28 |
| 206 | schrodinger/rc-slider (forked from: miskreant/rc-slider) React Slider 35 5 4 JavaScript MIT license 2016-07-20 19:49:07 |
| 206 | lh3/lv89 C implementation of the Landau-Vishkin algorithm 35 C++ MIT License 2022-04-08 14:32:42 |
| 206 | lh3/partig An experimental tool to estimate the similarity between all pairs of contigs bioinformatics, sequence-assembly 35 1 C 2021-04-12 04:34:01 |
| 206 | soedinglab/uniclust-pipeline 35 7 Shell GNU Affero General Public License v3.0 2018-04-24 09:16:56 |
| 206 | microsoft/LLM4ScientificDiscovery Call for participation in the impact of LLM for scientific discovery 35 4 4 MIT license |
| 206 | Azure/Bio-Compliancy 35 15 14 PowerShell MIT license |
| 207 | aqlaboratory/pnerfmachine-learning, molecular-dynamics, molecular-modeling, molecular-simulation, protein-structure, proteins 34 6 Python MIT License 2019-07-22 16:43:04 |
| 207 | deepchem/torchchem An experimental repo for experimenting with PyTorch models 34 13 Python MIT License 2023-03-24 23:13:19 |
| 207 | chembl/surechembl-data-client A collection of scripts for retrieving, storing, and querying SureChEMBL data. surechembl 34 17 Python MIT License 2022-11-04 19:05:28 |
| 207 | opentargets/genetics-sumstat-harmoniser Harmonise GWAS summary statistics against a reference VCF 34 5 Python Apache License 2.0 2021-06-15 12:41:52 |
| 207 | OBF/FALDO Feature Annotation Location Description Ontology biology, genomics, ontology, proteomics, uniprot 34 11 XSLT Creative Commons Zero v1.0 Universal 2020-01-21 01:29:22 |
| 208 | Gilead-BioStats/gsm Good Statistical Monitoring R Package 33 8 R Apache License 2.0 2024-06-06 14:03:31 |
| 208 | EBISPOT/ols4 Version 4 of the EMBL-EBI Ontology Lookup Service (OLS) bioinformatics, knowledge-graph, knowledge-management, knowledge-representation, ontologies, owl, rdf, semantic-web 33 15 Java Apache License 2.0 2024-06-04 10:08:27 |
| 208 | evo-design/protein-dpo Aligning protein generative models with experimental fitness 33 4 Python MIT License 2024-05-21 20:58:54 |
| 208 | soedinglab/spacepharer SpacePHARER CRISPR Spacer Phage-Host pAiRs findER bioinformatics, crispr, host-pathogen, sequence-analysis 33 4 C GNU General Public License v3.0 2024-05-08 13:45:17 |
| 209 | pharmaverse/tidytlg The goal of tidytlg is to generate tables, listings, and graphs (TLG) using Tidyverse. 32 7 Rich Text Format Other 2024-05-31 18:37:41 |
| 209 | phuse-org/rdf.cdisc.org PhUSE Semantic Technology Working Group CDISC Standards 32 14 Web Ontology Language 2015-09-08 17:22:18 |
| 209 | rdkit/UGM_2023 Materials from the 2023 RDKit UGM 32 15 Jupyter Notebook 2024-01-16 16:04:26 |
| 209 | rdkit/RDKitjs-legacy Obsolete codebase, please do not use. 32 12 HTML BSD 3-Clause "New" or "Revised" License 2023-01-03 22:52:57 |
| 209 | rdkit/CheTo CheTo - Chemical Topic Modeling 32 13 Jupyter Notebook BSD 3-Clause "New" or "Revised" License 2021-04-12 13:33:39 |
| 209 | pfizer-opensource/TorsionNet A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM 32 15 Jupyter Notebook MIT License 2023-03-13 10:38:57 |
| 209 | lh3/klib.nim Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang bioinformatics 32 1 Nim 2020-04-20 12:58:10 |
| 209 | lh3/asub A unified array job submitter for LSF, SGE/UGE and Slurm 32 15 Perl 2019-11-29 10:37:09 |
| 209 | scverse/napari-spatialdata Interactive visualization of spatial omics data napari, napari-plugin, spatial-analysis, spatial-omics, visualization 32 12 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 20:02:20 |
| 209 | chao1224/ProteinDTai4science, drug-design, foundation-model, large-language-model, llm, protein, protein-design, protein-editing, protein-sequence, protein-structure 32 4 6 Python MIT license 2024-03-26 16:21:22 |
| 210 | insightsengineering/r.pkg.template An opinionated R package template with CI/CD built-in git, github-actions, r, template 31 7 Shell Other 2024-06-05 15:37:35 |
| 210 | Sanofi-IADC/konviw Enterprise public viewer for your Confluence pages cms, confluence, headless-cms, viewer 31 8 TypeScript MIT License 2024-06-07 09:22:49 |
| 210 | lh3/gffio 31 1 C 2022-12-16 03:14:05 |
| 210 | lh3/pre-pe Preprocessing paired-end reads produced with experiment-specific protocols 31 2 C 2018-06-28 23:45:13 |
| 210 | OpenGene/VisualMSI Detect and visualize microsatellite instability(MSI) from NGS data 31 11 C++ MIT License 2019-06-04 03:14:17 |
| 210 | scverse/spatialdata-notebooks 31 15 Jupyter Notebook BSD 3-Clause "New" or "Revised" License 2024-05-28 14:29:43 |
| 211 | abbvie-external/OmicNavigator Open-Source Software for Omic Data Analysis and Visualization bioinformatics, genomics, omics, opencpu, r 30 8 R Other 2024-05-06 18:54:00 |
| 211 | bayer-science-for-a-better-life/phc-gnn Implementation of the Paper: "Parameterized Hypercomplex Graph Neural Networks for Graph Classification" by Tuan Le, Marco Bertolini, Frank Noé and Djork-Arné Clevert deep-learning, graph-classification, graph-neural-networks, graph-representation-learning, hypercomplex, neural-message-passing, quaternion 30 6 Python GNU General Public License v3.0 2021-09-03 09:43:57 |