This is an automatically generated1 list of recently updated 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 the ranked listing of open source software they share and which topics are covered by these software.
Taking the 200 last ones.
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
Warning
last updated date & time is not available for direct repositories links in sources. In these cases we use last release date if available or the UNIX epoch if not...
| Rank | Software |
|---|---|
| 1 | scverse/squidpy Spatial Single Cell Analysis in Python data-visualization, image-analysis, single-cell-genomics, single-cell-rna-seq, spatial-analysis, spatial-transcriptomics, squidpy 399 71 Python BSD 3-Clause "New" or "Revised" License 2024-06-08 21:22:47 |
| 2 | lh3/mssa-bench Evaluating the performance of multi-string SA construction suffix-array 1 C 2024-06-08 15:16:41 |
| 3 | deepchem/deepchem Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology biology, deep-learning, drug-discovery, hacktoberfest, materials-science, quantum-chemistry 5220 1626 Python MIT License 2024-06-08 13:03:11 |
| 4 | Exscientia/StableNetGuardOwl Perform stability tests for Neural Network Potentials molecular-dynamics, neural-network-potentials 5 Python MIT License 2024-06-08 12:18:24 |
| 5 | ebi-uniprot/protvar-fe ProtVar Project Front-end 4 2 TypeScript MIT License 2024-06-08 11:41:24 |
| 6 | shenwei356/bioconda-recipes (forked from: bioconda/bioconda-recipes) Conda recipes for the bioconda channel. 1 1 Shell MIT License 2024-06-08 10:18:32 |
| 7 | 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 |
| 8 | scverse/pertpy Perturbation Analysis in the scverse ecosystem. perturbation, scverse, single-cell 87 19 Python MIT License 2024-06-08 08:07:34 |
| 9 | Bioconductor/gha-build-rstudio-devel-amd64 C 2024-06-08 06:19:22 |
| 10 | Bioconductor/status.bioconductor.org Status page for Bioconductor based on cstate hugo site 2024-06-08 06:13:05 |
| 11 | Bioconductor/gha-build-jupyter-release-amd64 R 2024-06-08 06:11:50 |
| 12 | Bioconductor/gha-build-rstudio-release-amd64 R 2024-06-08 06:03:39 |
| 13 | insightsengineering/teal.gallery A Gallery of Exploratory Web Apps used for Analyzing Clinical Trial Data clinical-trials, nest, r, shiny, webapp 23 6 R Other 2024-06-08 03:47:14 |
| 14 | rdkit/rdkit The official sources for the RDKit library c-plus-plus, cheminformatics, python, rdkit 2483 845 HTML BSD 3-Clause "New" or "Revised" License 2024-06-08 03:18:22 |
| 15 | recursionpharma/EFAAR_benchmarking External repo for the EFAAR benchmarking paper 6 2 Python Apache License 2.0 2024-06-08 02:42:51 |
| 16 | pharmaverse/upptime Monitor pharmaverse.org uptime status-page, upptime, uptime-monitor Markdown MIT License 2024-06-08 01:11:53 |
| 17 | ome/upptime 📈 Uptime monitor and status page for OME, powered by @upptime status-page, upptime, uptime-monitor 1 1 Markdown MIT License 2024-06-08 00:59:27 |
| 18 | ome/openmicroscopy OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded … database, image, java, omero, python, server 187 100 Java GNU General Public License v2.0 2024-06-08 00:39:30 |
| 19 | Merck/psm3mkv psm3mkv: A package to evaluate the fit and efficiency of three state oncology cost-effectiveness model structures 8 2 R GNU General Public License v3.0 2024-06-08 00:39:26 |
| 20 | scverse/spatialdata An open and interoperable data framework for spatial omics data 186 34 Python BSD 3-Clause "New" or "Revised" License 2024-06-08 00:23:48 |
| 21 | Bioconductor/BiocSlack 1 CSS MIT License 2024-06-08 00:23:11 |
| 22 | genentech/set-dino Python Apache License 2.0 2024-06-07 23:54:30 |
| 23 | Bioconductor/BBS The Bioconductor Build System 9 10 Shell 2024-06-07 23:51:16 |
| 24 | genentech/quipcell Fine-scale cellular deconvolution based on Generalized Cross Entropy Jupyter Notebook MIT License 2024-06-07 23:27:17 |
| 25 | Merck/gsDesign2 Group Sequential Design Under Non-Proportional Hazards 15 6 R GNU General Public License v3.0 2024-06-07 23:23:06 |
| 26 | EBISPOT/GrEBI HPC pipeline for building integrated knowledge graphs from EBI resources 1 Rust 2024-06-07 23:01:45 |
| 27 | EBI-Metagenomics/assembly_uploader Upload of metagenome and metatranscriptome assemblies to ENA Python Apache License 2.0 2024-06-07 22:22:26 |
| 28 | insightsengineering/teal.modules.clinical Provides teal modules for the standard clinical trials outputs clinical-trials, modules, nest, outputs, r, shiny 29 13 R Other 2024-06-07 21:36:01 |
| 29 | insightsengineering/rtables Reporting tables with R pharmaceuticals, r, tables 213 49 R Other 2024-06-07 21:27:39 |
| 30 | deepchem/deepchem.github.io The DeepChem Website 2 11 HTML Apache License 2.0 2024-06-07 21:23:03 |
| 31 | Gilead-BioStats/gsmApp 1 1 HTML Apache License 2.0 2024-06-07 20:42:26 |
| 32 | genentech/gReLU gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences. 99 5 Python MIT License 2024-06-07 20:29:13 |
| 33 | GSK-Biostatistics/slushy 12 1 R Apache License 2.0 2024-06-07 20:20:21 |
| 34 | ebi-uniprot/QuickGoFE Front End component for QuickGo. 1 1 JavaScript 2024-06-07 20:06:16 |
| 35 | ome/bioformats Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software. bio-formats, format-converter, format-reader, image, java, life-sciences-image, lightsheet, metadata, whole-slide-imaging, wsi 367 239 Java GNU General Public License v2.0 2024-06-07 19:34:33 |
| 36 | Novartis/Causal-inference-in-RCTs This repository contains code examples for several methods in a Causal Inference in RCTs short course. 18 R MIT License 2024-06-07 19:03:09 |
| 37 | pharmaverse/admiralpeds Admiral Package Extension for Pediatric Clinical Trials cdisc, rstats 10 1 R Apache License 2.0 2024-06-07 18:56:49 |
| 38 | Gilead-BioStats/graphicalMCP Graphical Multiple Comparison Procedures 12 R Apache License 2.0 2024-06-07 18:43:27 |
| 39 | pharmaverse/admiral ADaM in R Asset Library cdisc, clinical-trials, open-source, r 207 53 R Apache License 2.0 2024-06-07 18:23:44 |
| 40 | 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 |
| 41 | opentargets/gentropy Open Targets python framework for post-GWAS analysis drug-discovery, genetics, gwas, open-source, pyspark, python 25 5 Jupyter Notebook Apache License 2.0 2024-06-07 17:59:12 |
| 42 | Bioconductor/Biostrings Efficient manipulation of biological strings bioconductor-package, core-package 48 16 R 2024-06-07 17:02:36 |
| 43 | genentech/jmpost 17 5 R 2024-06-07 16:30:15 |
| 44 | opentargets/platform-etl-backend 7 7 Scala Apache License 2.0 2024-06-07 16:26:15 |
| 45 | 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 |
| 46 | Bioconductor/workshop-contributions Repository for managing contributions to workshop.bioconductor.org 5 HTML 2024-06-07 16:19:57 |
| 47 | scverse/anndata Annotated data. anndata, bioinformatics, data-science, machine-learning, scanpy, scverse, transcriptomics 511 148 Python BSD 3-Clause "New" or "Revised" License 2024-06-07 16:03:50 |
| 48 | Bayer-Group/BIC-subscreenbeat-undefined R GNU General Public License v3.0 2024-06-07 15:56:38 |
| 49 | Sanofi-Public/RDCS-bulkRNASeq-pseudo_ordering Jupyter Notebook Other 2024-06-07 15:54:19 |
| 50 | EBISPOT/gwas-sumstats-harmoniser GWAS Summary Statistics Data Harmonisation 18 9 Python 2024-06-07 15:52:57 |
| 51 | EBISPOT/gwas-sumstats-service Summary statistics service 2 Python 2024-06-07 15:52:33 |
| 52 | ome/ome-ngff-validator Web page for validating OME-NGFF files ome-zarr 3 3 Svelte BSD 2-Clause "Simplified" License 2024-06-07 15:49:46 |
| 53 | opentargets/ot-ui-apps Open Targets Platform web applications embl-ebi, european-bioinformatics-institute, graphql, javascript, reactjs, turborepo, vitejs, webapp 4 9 JavaScript Apache License 2.0 2024-06-07 15:49:46 |
| 54 | Acellera/htmd HTMD: Programming Environment for Molecular Discovery automate, drug-discovery, htmd, molecular-simulations 250 58 Rich Text Format Other 2024-06-07 15:24:26 |
| 55 | openpharma/beeca lightweight R package around covariate adjustment 3 R GNU Lesser General Public License v3.0 2024-06-07 14:59:51 |
| 56 | biosustain/Maud Enzyme models that take into account kinetics, allostery and thermodynamics 26 2 Python GNU General Public License v3.0 2024-06-07 14:54:32 |
| 57 | biosustain/pankb The Pangenome Knowledge Base (PanKB) serves as an up-to-date resource for pangenomics research methods and the dissemination of results and currently offers basic pangenome characteristics and advanced pangenome analytics for six major biotech bacteria families. HTML 2024-06-07 14:40:18 |
| 58 | ome/ZarrReader 5 7 Java Other 2024-06-07 14:17:46 |
| 59 | pharmaverse/datacutr Apply a datacut to SDTM in R 12 2 R Apache License 2.0 2024-06-07 13:37:06 |
| 60 | ome/bio-formats-documentation Bio-Formats documentation bio-formats, documentation 8 15 Java BSD 2-Clause "Simplified" License 2024-06-07 13:35:07 |
| 61 | insightsengineering/rlistings Value formatting and ASCII rendering infrastructure for tables and listings. 21 5 R 2024-06-07 13:34:58 |
| 62 | EBI-Metagenomics/miassembler Nextflow Apache License 2.0 2024-06-07 13:30:39 |
| 63 | insightsengineering/osprey Community effort to collect TLG code and create a catalogue catalog, graphs, listings, nest, r, tables 4 1 R Other 2024-06-07 13:18:34 |
| 64 | ebi-gene-expression-group/atlas-web-single-cell Single Cell Expression Atlas web application 5 5 Java Apache License 2.0 2024-06-07 13:16:44 |
| 65 | EBI-Metagenomics/containers Repository to contain containers used by EBI Microbiome Informatics Python 2024-06-07 13:14:49 |
| 66 | samtools/bcftools This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html 626 241 C Other 2024-06-07 13:13:17 |
| 67 | insightsengineering/teal.slice Reproducible slice module for teal applications modules, nest, r, slice 11 5 R Other 2024-06-07 12:56:35 |
| 68 | insightsengineering/teal Exploratory Web Apps for Analyzing Clinical Trial Data clinical-trials, nest, r, shiny, webapp 164 29 R Other 2024-06-07 12:49:26 |
| 69 | Bayer-Group/BIC-megaplotbeat-undefined R GNU General Public License v3.0 2024-06-07 12:48:05 |
| 70 | openpharma/crmPack Object-Oriented Implementation of CRM Designs 19 9 HTML 2024-06-07 12:47:00 |
| 71 | Bioconductor/bioconductor.org Source code for the Bioconductor website bioconductor, website 22 39 HTML 2024-06-07 12:27:51 |
| 72 | Boehringer-Ingelheim/BayesianMCPMod 6 3 R Apache License 2.0 2024-06-07 12:20:06 |
| 73 | Bioconductor/bio-web-stats Code base for replacement of stats.bioconductor.org (download_stats) Python 2024-06-07 11:30:09 |
| 74 | EBISPOT/efo Github repo for the Experimental Factor Ontology (EFO) 54 14 Makefile 2024-06-07 11:24:56 |
| 75 | Bioconductor/2024-09-03-BiocProject-EuroBioc 2024-06-07 11:17:00 |
| 76 | Bioconductor/2024-09-02-RNASeq-EuroBioc 2024-06-07 11:16:18 |
| 77 | Bioconductor/2024-09-02-BiocIntro-EuroBioc 2024-06-07 11:15:18 |
| 78 | Boehringer-Ingelheim/dv.templates An R package template with built-in GitHub Actions-based CI/CD workflows. 1 R Other 2024-06-07 11:08:15 |
| 79 | pharmaverse/examples End to end examples of pharmaverse packages for common safety clinical reporting analyses 4 4 R Apache License 2.0 2024-06-07 10:26:38 |
| 80 | ebi-uniprot/protvar-be Backend REST API for protvar project 1 Java 2024-06-07 10:04:37 |
| 81 | scverse/scverse.github.io scverse.org website 1 6 SCSS 2024-06-07 10:01:31 |
| 82 | scverse/ecosystem-packages Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem) 15 34 Python BSD 3-Clause "New" or "Revised" License 2024-06-07 10:00:45 |
| 83 | Boehringer-Ingelheim/dv.manager 1 1 R Other 2024-06-07 09:49:40 |
| 84 | samtools/samtools Tools (written in C using htslib) for manipulating next-generation sequencing data 1572 572 C Other 2024-06-07 09:32:59 |
| 85 | ebi-uniprot/uniprot-manual 5 2024-06-07 09:31:53 |
| 86 | 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 |
| 87 | healx/terraform-provider-nftowerplatform-enablement, terraform, terraform-provider 4 Go Mozilla Public License 2.0 2024-06-07 08:51:37 |
| 88 | scverse/scanpy Single-cell analysis in Python. Scales to >1M cells. anndata, bioinformatics, data-science, machine-learning, python, scanpy, scverse, transcriptomics, visualize-data 1789 579 Python BSD 3-Clause "New" or "Revised" License 2024-06-07 08:43:34 |
| 89 | GSK-Biostatistics/beastt 1 R Apache License 2.0 2024-06-07 08:36:40 |
| 90 | AstraZeneca/biomedical-kg-topological-imbalance Code to accompany the "Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs" (Briefings in Bioinformatics, 2022) drug-discovery, drug-discovery-knowledge-graph, knowledge-graph, knowledge-graph-completion, target-prediction 14 Jupyter Notebook Apache License 2.0 2024-06-07 07:59:07 |
| 91 | bedapub/splicekit splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq 14 3 Python 2024-06-07 07:30:05 |
| 92 | calico/baskerville Machine learning methods for DNA sequence analysis. 21 3 Python Apache License 2.0 2024-06-07 03:34:55 |
| 93 | pharmaverse/admiraldev Development Tools for the admiral family 15 6 R Apache License 2.0 2024-06-07 00:48:38 |
| 94 | enveda/ccs-prediction Evaluating the generalizability of graph neural networks for predicting collision cross section collision-cross-section, deep-learning, gnn, mass-spectrometry 3 2 Jupyter Notebook GNU General Public License v2.0 2024-06-06 23:56:00 |
| 95 | enveda/np-clinical-trials Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process" clinical-trials, drug-discovery, natural-products 1 1 Jupyter Notebook GNU General Public License v3.0 2024-06-06 23:53:20 |
| 96 | 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 |
| 97 | pharmaverse/sdtmchecks Analysis facing checks for SDTM data 20 7 R Other 2024-06-06 23:20:50 |
| 98 | 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 |
| 99 | schrodinger/pymol-open-source Open-source foundation of the user-sponsored PyMOL molecular visualization system. 1071 260 C Other 2024-06-06 19:36:48 |
| 100 | insitro/redun Yet another redundant workflow engine aws, bioinformatics, data-engineering, data-science, docker, etl, gcp, ml, python, workflow-engine 489 40 Python Apache License 2.0 2024-06-06 18:52:56 |
| 101 | genentech/beignet A standard library for biological research. 11 4 Python MIT License 2024-06-06 18:16:34 |
| 102 | Merck/wpgsd Weighted parametric group sequential design 1 2 R GNU General Public License v3.0 2024-06-06 18:14:32 |
| 103 | ome/napari-ome-zarr A napari plugin for zarr backed OME-NGFF images napari-plugin, ngff, python, zarr 24 20 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 17:42:54 |
| 104 | insightsengineering/scda.test Package that runs tests for tern and scda clinical-trials, graphs, listings, nest, outputs, r, tables 2 R Other 2024-06-06 16:33:51 |
| 105 | pharmaverse/admiralophtha Ophthalmology package extension of admiral 13 4 R Apache License 2.0 2024-06-06 16:04:56 |
| 106 | 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 |
| 107 | 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 |
| 108 | ome/ome2024-ngff-challenge Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data 2 2024-06-06 15:47:53 |
| 109 | Bayer-Group/BayerCLAW BayerCLAW workflow orchestration system for AWS aws, bayer-not-classified, bayer-reg-none, beat-not-applicable, pipeline, workflow 18 8 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 15:45:06 |
| 110 | samtools/htslib C library for high-throughput sequencing data formats bam, bcf, bioinformatics, cram, htslib, ngs, sam, vcf 779 448 C Other 2024-06-06 15:40:15 |
| 111 | EBISPOT/scxa_2_cxg 1 Python Apache License 2.0 2024-06-06 14:59:14 |
| 112 | ebi-uniprot/uniprot-core UniProt core domain model, parser and xml 4 Java Apache License 2.0 2024-06-06 14:16:43 |
| 113 | ebi-uniprot/uniprot-store This project is for building uniprot search engine lifescience, protein, solrcloud, spring-batch, spring-boot, voldemort 3 Java Apache License 2.0 2024-06-06 14:16:40 |
| 114 | ebi-uniprot/uniprot-rest-api UniProt Website development for Back end services 4 3 Java Apache License 2.0 2024-06-06 14:16:37 |
| 115 | Gilead-BioStats/gsm Good Statistical Monitoring R Package 33 8 R Apache License 2.0 2024-06-06 14:03:31 |
| 116 | ome/omero-web Django-based OMERO.web client client, django, omero, python, web 15 28 Python 2024-06-06 14:01:23 |
| 117 | Sanofi-Public/LipoBART 3 Jupyter Notebook Other 2024-06-06 13:50:10 |
| 118 | recursionpharma/gflownet GFlowNet library specialized for graph & molecular data deep-learning, gflownet, graph-neural-network, pytorch 168 34 Python MIT License 2024-06-06 13:29:06 |
| 119 | openpharma/savvyr savvyr: Estimation of adverse event probabilities 4 1 R 2024-06-06 13:23:46 |
| 120 | insightsengineering/teal.modules.hermes RNA-seq analysis modules to add to a teal application modules, r, rna-seq-analysis, shiny 7 1 R Other 2024-06-06 13:16:21 |
| 121 | EBIBioSamples/biosamples-v4 The source code for the new version of the EMBL-EBI BioSamples database 10 9 Java Apache License 2.0 2024-06-06 13:05:00 |
| 122 | EBI-Metagenomics/amplicon-pipeline 4 Nextflow Apache License 2.0 2024-06-06 13:00:52 |
| 123 | scverse/cookiecutter-scverse-instance Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template. 1 2 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 12:59:45 |
| 124 | scverse/cookiecutter-scverse Cookiecutter template for scverse 66 8 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 12:59:20 |
| 125 | ome/ome-zarr-py Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud. ngff, ome, ome-zarr, zarr 143 51 Python Other 2024-06-06 12:51:57 |
| 126 | biosustain/datacatalog-documentation 2 2024-06-06 12:29:37 |
| 127 | EBI-Metagenomics/emgapi MGnify RESTful API api, django, django-rest-framework, jsonapi, resource 10 Python Apache License 2.0 2024-06-06 12:28:55 |
| 128 | insightsengineering/teal.modules.general General Purpose Teal Modules general-purpose, modules, nest, r, shiny 9 6 R Other 2024-06-06 12:24:10 |
| 129 | insightsengineering/teal.goshawk Modules that produce web interfaces through which longitudinal visualizations can be dynamically modules, nest, r 3 2 R Other 2024-06-06 12:21:06 |
| 130 | johnsonandjohnson/vxnaid Vxnaid™ is a digital platform that supports correct vaccine administration & efficient vaccination campaigns. 1 1 Kotlin Apache License 2.0 2024-06-06 12:19:14 |
| 131 | Bioconductor/CSAMA Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology 89 45 HTML 2024-06-06 12:04:08 |
| 132 | insightsengineering/teal.reporter Create and preview reports with Shiny modules nest, r, reporting, shiny 8 8 R Other 2024-06-06 11:59:45 |
| 133 | biosustain/dgfreg Regression models of biochemical formation energies 2 Jupyter Notebook MIT License 2024-06-06 11:54:56 |
| 134 | biosustain/dsp_nf-metagenomics Shotgun metagenomics pipeline to process microbiome samples metagenomics, nextflow-pipeline 1 Shell GNU General Public License v3.0 2024-06-06 11:48:39 |
| 135 | insightsengineering/tern.mmrm Create MMRM TLGs using lme4 and tern graphs, listings, r, statistical-engineering, tables 6 1 R 2024-06-06 11:43:17 |
| 136 | insilicomedicine/precious3-gpt 2024-06-06 11:40:32 |
| 137 | EliLillyCo/ErlWoodKNIME This is the LRL_ErlWoodKNIME Repo lrl 4 5 Java GNU General Public License v3.0 2024-06-06 11:38:11 |
| 138 | insightsengineering/tern.rbmi Create TLGs using rbmi and tern graphs, listings, r, tables 3 1 R Other 2024-06-06 11:34:18 |
| 139 | EBI-Metagenomics/HoloFoodR R interface for HoloFood resource 1 R Artistic License 2.0 2024-06-06 11:20:36 |
| 140 | insightsengineering/teal.osprey Community efforts to collect teal modules for TLGs defined in the osprey package modules, nest, r 5 2 R Other 2024-06-06 11:17:18 |
| 141 | opentargets/evidence_datasource_parsers script to convert phewascatalog database to JSONs, with ENSGIDs and EFO ids. 6 2 Python Apache License 2.0 2024-06-06 11:01:45 |
| 142 | Acellera/acegen-open Language models for drug discovery using torchrl 29 7 Python MIT License 2024-06-06 10:48:44 |
| 143 | scverse/spatialdata-plot Static plotting for spatialdata 24 14 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 10:42:46 |
| 144 | johnsonandjohnson/openmrs-distro-vxnaid Cintains the Vxnaid distribution application for OpenMRS. It has been tailored for quick-evaluation of Vxnaid features and as a base for production builds. 2 Shell Other 2024-06-06 10:09:43 |
| 145 | EBI-Metagenomics/genomes-catalogue-pipeline MGnify genome analysis pipeline 93 21 Python Other 2024-06-06 09:44:21 |
| 146 | insightsengineering/verdepcheck An R package that tests your R package against the min/max versions of specified dependencies check, devtools, r, testing, utils 1 R Other 2024-06-06 09:39:05 |
| 147 | johnsonandjohnson/openmrs-module-vxnaid-biometric Module for OpenMRS to provide REST APIs to retrieve configurations, register and match participants using bio-graphich and biometric information and, match a participant, create/update visit and creating encounters. 1 Java Other 2024-06-06 08:35:14 |
| 148 | EBISPOT/gwas-sumstats-tools 7 1 Python Apache License 2.0 2024-06-06 08:29:29 |
| 149 | servierhub/top-life-sciences Top Life Sciences open-source software ai, awesome, awesome-list, awesome-lists, bioinformatics, biology, biology-ai, computational-biology, computational-chemistry, ebiology, life-sciences, lifescience, lifesciences, pharma, pharmaceuticals, servier 1 2024-06-06 07:56:59 |
| 150 | ceva-sante-animale/upload-production-reports Python 2024-06-06 07:41:39 |
| 151 | pharmaverse/pharmaversesdtm Test SDTM data for use within the pharmaverse family of packages 12 1 R Apache License 2.0 2024-06-06 07:11:38 |
| 152 | pharmaverse/pharmaverseadam Test ADaM data for use with pharmaverse 9 2 R Apache License 2.0 2024-06-06 07:07:35 |
| 153 | samtools/hts-specs Specifications of SAM/BAM and related high-throughput sequencing file formats 627 173 TeX 2024-06-06 06:50:26 |
| 154 | nn-dma/generate-verification-report Takes metadata and test results as input and generates a verification report as output. 1 Go 2024-06-06 06:29:54 |
| 155 | scverse/scirpy A scanpy extension to analyse single-cell TCR and BCR data. 202 31 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 06:21:35 |
| 156 | pharmaverse/blog Blogging on the latest, greatest and most spectacular stuff happening around the pharmaverse 17 7 R Apache License 2.0 2024-06-06 05:40:58 |
| 157 | AstraZeneca/persist-seq-galaxy-tools-setup Python 2024-06-06 04:09:28 |
| 158 | Merck/metalite.sl An R package designed for the analysis & reporting of subject baseline characteristics in clinical trials. R GNU General Public License v3.0 2024-06-06 03:12:19 |
| 159 | owkin/PyDESeq2 A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. bioinformatics, differential-expression, python, rna-seq, transcriptomics 533 58 Python MIT License 2024-06-06 01:43:52 |
| 160 | ome/bio-formats-build Bio-Formats top-level build for all components bio-formats, build, meta-repo 10 Shell 2024-06-05 23:58:07 |
| 161 | insightsengineering/ci-images Insights Engineering Container Images docker, images, r, reproducibility, rocker 10 2 R 2024-06-05 19:44:30 |
| 162 | insightsengineering/tlg-catalog A catalog of Tables, Listings and Graphs (TLGs) created with NEST R packages 17 4 JavaScript Other 2024-06-05 18:04:25 |
| 163 | hail-is/hail Cloud-native genomic dataframes and batch computing bioinformatics, genetics, genomics, gwas, hail, python, software, vcf 946 238 55 Python MIT license 2024-06-05 17:48:05 |
| 164 | insightsengineering/biomarker-catalog Biomarker Analysis Templates of Tables And Graphs 📊 5 SCSS 2024-06-05 17:34:30 |
| 165 | scverse/scvi-tools Deep probabilistic analysis of single-cell and spatial omics data cite-seq, deep-generative-model, deep-learning, human-cell-atlas, scrna-seq, scverse, single-cell-genomics, single-cell-rna-seq, variational-autoencoder, variational-bayes 1149 342 Python BSD 3-Clause "New" or "Revised" License 2024-06-05 17:01:13 |
| 166 | Novartis/bamdd Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms bayesian, brms, clinical, stan 14 2 TeX GNU General Public License v2.0 2024-06-05 16:45:28 |
| 167 | Bioconductor/SparseArray High-performance sparse data representation and manipulation in R bioconductor-package, core-package 6 2 C 2024-06-05 16:35:22 |
| 168 | Bayer-Group/react-color-a11y React higher-order component to automatically enforce color accessibility 5 1 TypeScript MIT License 2024-06-05 16:08:52 |
| 169 | EBI-Metagenomics/mettannotator 1 2 Python Apache License 2.0 2024-06-05 16:05:29 |
| 170 | Bayer-Group/MOCCAbeat-undefined 1 1 Python MIT License 2024-06-05 15:46:04 |
| 171 | shenwei356/memusg (forked from: drewkett/memusg) A 'time'-like utility for Unix that measures peak memory usage 18 5 Python 2024-06-05 15:38:46 |
| 172 | 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 |
| 173 | EBISPOT/gwas-curation-ui The New Curation Front End interface for the GWAS Catalog TypeScript 2024-06-05 15:29:17 |
| 174 | neurogenomics/MotifStats Package for integrating peak and motif positions 1 1 R GNU General Public License v3.0 2024-06-05 15:04:57 |
| 175 | EBISPOT/gwas-utils Collection of tools and scripts to manage GWAS Catalog related infrastructure. data-release, quality-control, toolbox 6 2 Python 2024-06-05 14:59:20 |
| 176 | insightsengineering/chevron Standard TLGs For Clinical Trials Reporting clinical-trials, graphs, listings, nest, r, reporting, tables 7 R Other 2024-06-05 14:57:39 |
| 177 | regeneron-mpds/wipperman_digital_wearable_insole_ML Jupyter Notebook Other 2024-06-05 14:10:40 |
| 178 | opentargets/platform-api GraphQL and Rest API rewrite of the current Open Targets platform API 8 4 Scala Apache License 2.0 2024-06-05 13:59:57 |
| 179 | ome/omero-scripts Core OMERO Scripts omero, python, scripts 11 32 Python 2024-06-05 13:26:28 |
| 180 | OpenBioSim/somd2 SOMD2 molecular dynamics for free energy calculations 6 2 Python GNU General Public License v3.0 2024-06-05 13:11:48 |
| 181 | AstraZeneca/MVDA_exploration_tools Multivariate data analysis (MVDA) exploration tool is a Python library utilizing the scikit-learn library for partial least squares (PLS) and principal components analysis (PCA). 4 1 Jupyter Notebook Apache License 2.0 2024-06-05 13:09:10 |
| 182 | insightsengineering/rbmi Reference based multiple imputation R package 13 4 R Other 2024-06-05 12:08:47 |
| 183 | pharmaverse/admiralonco Oncology extension package for ADaM in R Asset Library (admiral) 27 8 R Other 2024-06-05 11:01:40 |
| 184 | ome/ome-codecs OME image compression (coder-decoder implementations) codecs 4 11 Java Other 2024-06-05 10:15:54 |
| 185 | EBIBioStudies/biostudies-backend-services Repository for BioStudies backend services 3 1 Kotlin 2024-06-05 09:45:26 |
| 186 | ome/omero-figure An OMERO.web app for creating Figures from images in OMERO omero, webapp 14 30 JavaScript GNU Affero General Public License v3.0 2024-06-05 09:34:35 |
| 187 | neurogenomics/HPOExplorer Functions for working with the Human Phenotype Ontology data bioinformatics, clinical-genomics, genetics, human-phenotype-ontology, ontologies, phenome, r-package, rare-disease 2 1 R 2024-06-05 09:34:08 |
| 188 | EBI-Metagenomics/mgnifams-site 1 1 JavaScript MIT License 2024-06-05 09:33:07 |
| 189 | EBI-Metagenomics/shallowmapping Shallow-shotgun mapping pipeline Python MIT License 2024-06-05 08:45:30 |
| 190 | Bioconductor/CSAMA_website (forked from: Huber-group-EMBL/CSAMA_website) Website for CSAMA 1 CSS MIT license 2024-06-05 07:48:44 |
| 191 | insightsengineering/teal.modules.bsafe Teal modules for bsafe clinical-trials, r 1 R Other 2024-06-05 07:48:32 |
| 192 | EBISPOT/gwas-curation-service Java 2024-06-05 07:07:14 |
| 193 | EBISPOT/gwasdepo-commons Java 2024-06-05 07:06:44 |
| 194 | Merck/forestly Interactive forest plot for adverse events analysis 10 3 R GNU General Public License v3.0 2024-06-05 03:40:44 |
| 195 | chao1224/Geom3D Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023 3d, 3d-structures, ai4science, biology, chemistry, crystals, drugs, equivariance, geometry, group, invariance, material, molecules, physics, proteins, symmetry 105 9 2 Python MIT license 2024-06-05 03:18:58 |
| 196 | ome/www.openmicroscopy.org OME main website jekyll-site, ome 5 22 HTML Creative Commons Attribution 4.0 International 2024-06-05 00:24:54 |
| 197 | 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 |
| 198 | AstraZeneca/runnable Runnable 38 4 Python Apache License 2.0 2024-06-04 20:42:58 |
| 199 | samtools/htsjdk A Java API for high-throughput sequencing data (HTS) formats. bam, cram, dna, fasta, genomics, java, java-api, ngs, sam, sequencing, vcf 274 244 Java 2024-06-04 18:40:43 |
| 200 | insightsengineering/cardx R Package to Supplement ARD Functions Found in {cards} r 1 R Other 2024-06-04 18:09:50 |