This is an automatically generated1 list of open source software from PRISME Forum members that are present on GitHub. It will be periodically refreshed from these sources' repositories.
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| Rank | Software |
|---|---|
| 1 | 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 |
| 2 | AstraZeneca/awesome-explainable-graph-reasoning A collection of research papers and software related to explainability in graph machine learning. awesome-list, deep-learning, explainable-ai, explainable-ml, graph, graph-algorithms, graphml 1941 129 Apache License 2.0 2022-04-04 14:54:08 |
| 3 | AstraZeneca/chemicalx A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022) biology, chemistry, deep-chemistry, deep-learning, drug, drug-discovery, drug-interaction, drug-pair, geometric-deep-learning, geometry, graph-neural-network, machine-learning, pharma, polypharmacy, pytorch, smiles, smiles-strings, torch, torchdrug 701 89 Python Apache License 2.0 2023-09-11 08:01:43 |
| 4 | MolecularAI/aizynthfinder A tool for retrosynthetic planning astrazeneca, chemical-reactions, cheminformatics, monte-carlo-tree-search, neural-networks, reaction-informatics 548 125 Python MIT License 2024-06-03 13:34:33 |
| 5 | biosustain/potion Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine flask, flask-extensions, mongoengine, peewee, sqlalchemy 488 51 Python Other 2019-04-23 17:00:39 |
| 6 | MolecularAI/GraphINVENT Graph neural networks for molecular design. 356 74 Python MIT License 2023-03-11 11:55:32 |
| 7 | MolecularAI/Reinventastrazeneca, cheminformatics, denovo-design, neural-networks, reinforcement-learning, transfer-learning 332 108 Python Apache License 2.0 2023-10-19 05:26:16 |
| 8 | Roche/pyreadstat Python package to read sas, spss and stata files into pandas data frames. It is a wrapper for the C library readstat. conversion, pandas-dataframe, python, readstat, sas7bdat, spss, stata-files 303 55 C Other 2024-06-04 09:55:07 |
| 9 | AstraZeneca/rexmex A general purpose recommender metrics library for fair evaluation. coverage, deep-learning, evaluation, machine-learning, metric, metrics, mrr, personalization, precision, rank, ranking, recall, recommender, recommender-system, recsys, rsquared 275 25 Python 2023-08-22 09:22:20 |
| 10 | MolecularAI/REINVENT4 AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization. ai, astrazeneca, cheminformatics, chemistry, deep-learning, denovo-design, drug-design, drug-discovery, generative-ai, ml, molecule-generation, neural-networks, reinforcement-learning, transfer-learning 247 57 Python Apache License 2.0 2024-04-27 11:00:08 |
| 11 | rdkit/rdkit-tutorials Tutorials to learn how to work with the RDKit 239 71 Jupyter Notebook Other 2023-03-19 13:36:55 |
| 12 | insightsengineering/rtables Reporting tables with R pharmaceuticals, r, tables 213 49 R Other 2024-06-07 21:27:39 |
| 13 | Bayer-Group/cloudformation-template-generator A type-safe Scala DSL for generating CloudFormation templates 211 71 Scala BSD 3-Clause "New" or "Revised" License 2022-07-29 11:32:04 |
| 14 | Bayer-Group/etcd-aws-cluster A container to assist in managing a etcd2 cluster from an Amazon auto scaling group 202 102 Shell BSD 3-Clause "New" or "Revised" License 2017-02-01 01:09:05 |
| 15 | rdkit/mmpdb A package to identify matched molecular pairs and use them to predict property changes. 195 53 Python Other 2024-04-30 10:55:30 |
| 16 | bioinform/somaticseq An ensemble approach to accurately detect somatic mutations using SomaticSeq cancer-genomics, somatic-variants 189 53 Python BSD 2-Clause "Simplified" License 2024-05-30 07:55:34 |
| 17 | MolecularAI/Chemformer 188 34 Python Apache License 2.0 2024-05-29 14:43:33 |
| 18 | AstraZeneca-NGS/VarDict VarDict 186 60 Perl MIT License 2024-01-05 14:06:13 |
| 19 | AstraZeneca/awesome-drug-discovery-knowledge-graphs A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022) awesome-list, drug-discovery, drug-discovery-knowledge-graph, knowledge-graph 177 19 Apache License 2.0 2023-09-10 16:33:40 |
| 20 | rgcgithub/regenie regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. 172 49 C++ Other 2024-04-03 13:52:31 |
| 21 | bioinform/neusomatic NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection convolutional-neural-networks, deep-learning, genomics, somatic-variants 167 50 Python Other 2021-12-23 10:41:50 |
| 22 | 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 |
| 23 | MolecularAI/ReinventCommunityastrazeneca, cheminformatics, denovo-design, jupyter-notebook, neural-networks, reinforcement-learning, transfer-learning 145 57 Jupyter Notebook MIT License 2022-04-22 16:44:35 |
| 24 | Novartis/tidymodules An Object-Oriented approach to Shiny modules communication, inheritance, oop, r, shiny, shiny-modules, tidy-operators 141 11 R Other 2023-02-23 15:04:31 |
| 25 | MolecularAI/deep-molecular-optimization Molecular optimization by capturing chemist’s intuition using the Seq2Seq with attention and the Transformer molecular-optimization, multi-property-optimization, seq2seq, transformer 139 36 Python Apache License 2.0 2023-03-16 07:05:06 |
| 26 | AstraZeneca/SubTab The official implementation of the paper, "SubTab: Subsetting Features of Tabular Data for Self-Supervised Representation Learning" contrastive-learning, multi-view-learning, representation-learning, self-supervised-learning, tabular-data 138 20 Python Apache License 2.0 2022-07-01 09:03:38 |
| 26 | johnsonandjohnson/Bodiless-JS Framework for building editable websites on the JAMStack 138 59 TypeScript Apache License 2.0 2024-01-24 03:00:32 |
| 27 | AstraZeneca/awesome-shapley-value Reading list for "The Shapley Value in Machine Learning" (JCAI 2022) artificial-intelligence, data-science, deep-learning, explainability, explainable, explainable-ai, explainable-artificial-intelligence, explainable-ml, lime, machine-learning, owen-value, shap, shapley, shapley-additive-explanations, shapley-decomposition, shapley-q-value, shapley-value, xai 134 10 Apache License 2.0 2022-08-08 08:53:10 |
| 28 | Merck/BioPhi BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design. antibody, humanization, humanness, oasis, sapiens 129 44 Python MIT License 2024-06-03 07:17:18 |
| 29 | AstraZeneca-NGS/VarDictJava VarDict Java port 127 52 Java MIT License 2024-01-05 14:03:51 |
| 30 | rdkit/rdkit-js A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit . cheminformatics, drug-discovery, javascript, molecule, molecule-viewer, molecule-visualization, node-js, npm, rdkit, react, wasm 123 35 Dockerfile BSD 3-Clause "New" or "Revised" License 2024-06-01 09:54:52 |
| 31 | Roche/BalancedLossNLP 118 23 Jupyter Notebook Other 2023-06-12 21:51:15 |
| 32 | Merck/deepbgc BGC Detection and Classification Using Deep Learning bidirectional-lstm, biosynthetic-gene-clusters, deep-learning, deepbgc, natural-products, pfam2vec, python, synthetic-biology 117 26 Jupyter Notebook MIT License 2023-11-11 12:48:56 |
| 33 | genentech/equifold Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation machine-learning, proteins, structural-biology, structure-prediction 116 15 Python Apache License 2.0 2023-01-08 19:51:30 |
| 34 | biosustain/cameo cameo - computer aided metabolic engineering & optimization 113 42 Python Apache License 2.0 2022-11-07 14:54:19 |
| 35 | Merck/Halyard Halyard is an extremely horizontally scalable Triplestore with support for Named Graphs, designed for integration of extremely large Semantic Data Models, and for storage and SPARQL 1.1 querying of the whole Linked Data universe snapshots. 107 17 Java Apache License 2.0 2023-01-23 16:59:32 |
| 36 | bayer-science-for-a-better-life/Img2Mol 103 41 Jupyter Notebook Apache License 2.0 2023-03-24 18:07:41 |
| 37 | Biogen-Inc/tidyCDISC Demo the app here: https://bit.ly/tidyCDISC_app pharma, r, rinpharma, rstats 102 38 R GNU Affero General Public License v3.0 2023-09-22 15:18:20 |
| 38 | MolecularAI/DockStream DockStream: A Docking Wrapper to Enhance De Novo Molecular Design astrazeneca, chemoinformatics, denovo-design, jupyter-notebook, molecular-docking, reinforcement-learning 100 30 Python Apache License 2.0 2023-03-16 07:07:10 |
| 38 | Bayer-Group/paquo PAthological QUpath Obsession - QuPath and Python conversations digital-pathology, python, qupath 100 16 Python GNU General Public License v3.0 2024-06-02 18:21:27 |
| 39 | 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 |
| 40 | Sanofi-Public/CodonBERT Repository for mRNA Paper and CodonBERT publication. 94 14 Python Other 2024-05-03 19:24:06 |
| 41 | AstraZeneca/onto_merger OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain. algorithm, alignment, biological-networks, biology, graph, kg, knowledge, knowledge-graph, mapping, ontology, ontology-alignment 89 5 HTML Apache License 2.0 2024-01-11 19:22:08 |
| 42 | Sanofi-IADC/whispr Open source event, comment and alert processing hub created by Sanofi IADC 88 8 TypeScript MIT License 2024-06-04 12:01:03 |
| 43 | 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 |
| 43 | bioinform/rnacocktailrna-seq 86 48 Jupyter Notebook Other 2020-11-11 06:42:10 |
| 44 | EliLillyCo/LillyMol LillyMol Public Code 82 29 C++ Apache License 2.0 2024-03-15 21:39:57 |
| 45 | Novartis/YADA Open-source Data Ops 81 21 Java Apache License 2.0 2022-11-16 09:27:33 |
| 46 | AstraZeneca/biology-for-ai learning biology syllabus, geared for machine learning folks 78 10 2022-12-05 16:29:03 |
| 46 | AstraZeneca-NGS/reference_data Reference data: BED files, genes, transcripts, variations. 78 28 Python 2017-11-28 14:42:42 |
| 46 | 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 |
| 47 | 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 |
| 48 | 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 |
| 49 | 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 |
| 49 | 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 |
| 50 | 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 |
| 50 | 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 |
| 51 | genentech/pviz Pviz 68 22 JavaScript Other 2016-09-13 06:28:27 |
| 52 | 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 |
| 52 | 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 |
| 53 | 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 |
| 54 | GSK-Biostatistics/tfrmt r package for formatting tables 63 3 R Other 2024-04-16 12:52:10 |
| 54 | Merck/DeepNeuralNet-QSAR 63 27 Python GNU General Public License v3.0 2018-10-24 20:07:27 |
| 55 | 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 |
| 56 | molecularinformatics/Computational-ADME 58 13 Python MIT License 2024-02-15 15:20:55 |
| 57 | 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 |
| 58 | 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 |
| 58 | 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 |
| 58 | 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 |
| 59 | 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 |
| 60 | 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 |
| 60 | 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 |
| 60 | rdkit/django-rdkit 53 26 Python BSD 3-Clause "New" or "Revised" License 2024-04-29 21:54:50 |
| 60 | 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 |
| 61 | 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 |
| 62 | 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 |
| 62 | MolecularAI/Lib-INVENT 51 30 Jupyter Notebook Apache License 2.0 2023-03-11 11:39:46 |
| 62 | 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 |
| 62 | rdkit/UGM_2020 Materials from the (virtual) 2020 RDKit UGM 51 22 Jupyter Notebook 2020-10-26 03:39:26 |
| 62 | genentech/sVAE 51 5 Python Apache License 2.0 2023-07-21 14:07:07 |
| 63 | 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 |
| 64 | Bayer-Group/stax AWS CloudFormation stack manager 49 8 Shell Other 2015-08-31 18:03:41 |
| 64 | rdkit/conda-rdkit Conda build recipe for the rdkit 49 30 C 2022-01-11 05:44:22 |
| 65 | 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 |
| 66 | EliLillyCo/pytest-wdl WDL plugin for pytest 47 8 Python Apache License 2.0 2023-08-01 23:14:28 |
| 66 | 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 |
| 67 | 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 |
| 67 | 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 |
| 68 | Bayer-Group/column-resizer Adds resizable columns to tables 45 23 JavaScript Other 2023-10-26 02:34:31 |
| 69 | 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 |
| 69 | Bayer-Group/stoop Monadic Scala API for CouchDB beat-not-applicable 44 4 Scala Other 2015-01-13 17:13:53 |
| 69 | 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 |
| 69 | rdkit/homebrew-rdkit Homebrew formula for rdkit 44 19 Ruby 2022-06-22 08:12:35 |
| 70 | 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 |
| 71 | rdkit/UGM_2022 Materials from the 2022 UGM 42 14 Jupyter Notebook 2022-10-31 16:30:51 |
| 72 | 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 |
| 73 | 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 |
| 73 | 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 |
| 73 | 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 |
| 73 | rdkit/UGM_2021 Materials from the (virtual) 2021 RDKit UGM 40 18 Jupyter Notebook 2021-10-22 11:44:33 |
| 74 | 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 |
| 74 | Roche/foxops Templating for Git Repositories 39 6 Python Apache License 2.0 2024-05-27 19:22:11 |
| 75 | AstraZeneca/runnable Runnable 38 4 Python Apache License 2.0 2024-06-04 20:42:58 |
| 75 | Bayer-Group/kamon-prometheus A Kamon backend to support Prometheus 38 19 HTML Other 2017-06-22 19:33:30 |
| 76 | rdkit/shape-it Updated version of Silicos-it's shape-based alignment tool 37 11 C++ MIT License 2024-03-23 04:22:24 |
| 76 | biosustain/shu Multi-dimensional, trans-omics metabolic maps. metabolism, systems-biology, visualization 37 Rust Apache License 2.0 2024-03-18 13:59:48 |
| 77 | Novartis/torchsurv Deep survival analysis made easy deep-learning, pytorch, survival-analysis 35 5 Python MIT License 2024-04-29 18:57:39 |
| 77 | Novartis/ontobrowser OntoBrowser is a web-based application for managing ontologies 35 9 Java Apache License 2.0 2023-02-15 10:40:14 |
| 77 | rdkit/UGM_2016 Materials from the 2016 RDKit UGM 35 21 Jupyter Notebook 2017-01-09 08:40:28 |
| 78 | Gilead-BioStats/gsm Good Statistical Monitoring R Package 33 8 R Apache License 2.0 2024-06-06 14:03:31 |
| 79 | rdkit/UGM_2023 Materials from the 2023 RDKit UGM 32 15 Jupyter Notebook 2024-01-16 16:04:26 |
| 79 | 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 |
| 79 | rdkit/CheTo CheTo - Chemical Topic Modeling 32 13 Jupyter Notebook BSD 3-Clause "New" or "Revised" License 2021-04-12 13:33:39 |
| 79 | 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 |
| 80 | 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 |
| 80 | 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 |
| 81 | 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 |
| 81 | 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 |
| 81 | Novartis/yap High throughput, pain-free big data pipelines. 30 7 Python Apache License 2.0 2017-03-11 21:07:30 |
| 81 | genentech/iterative-perturb-seq Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors 30 2 Jupyter Notebook Apache License 2.0 2024-05-25 02:27:44 |
| 82 | AstraZeneca/kgem-in-drug-discovery Code to accompany the "Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery" manuscript (Artificial Intelligence in the Life Sciences, 2022) drug-discovery, drug-discovery-knowledge-graph, knowledge-graph, knowledge-graph-embedding-models, knowledge-graph-embeddings, target-prediction 29 6 Python Apache License 2.0 2024-05-21 08:58:54 |
| 82 | AstraZeneca/StarGazer StarGazer is a tool designed for rapidly assessing drug repositioning opportunities. It combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits. 29 13 Python Apache License 2.0 2023-08-14 22:36:23 |
| 82 | GSK-AI/meta-learning-qsar Meta-Learning GNN Initializations for Low-Resource Molecular Property Prediction 29 4 Python MIT License 2020-07-20 18:24:17 |
| 82 | Merck/pkglite Compact Package Representations clinical-trials, ectd, package, packaging-tool, pharmaverse, r 29 4 R GNU General Public License v3.0 2024-04-26 01:43:37 |
| 82 | Novartis/pQSAR Massively multitask stacked model for predicting activity of thousands of biological assays 29 6 Python Apache License 2.0 2021-08-24 18:01:38 |
| 82 | 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 |
| 83 | Novartis/pisces PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon. bioinformatics, bioinformatics-pipeline, rnaseq, rnaseq-pipeline, salmon, transcriptomics 28 3 Python Apache License 2.0 2024-05-28 13:38:43 |
| 83 | Novartis/pqsar2cpd pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules. 28 6 Python MIT License 2023-07-12 09:10:24 |
| 83 | openPfizer/DigitalHealthData Visualization package for Apple Watch data collected by Healthkit 28 5 Python Apache License 2.0 2019-04-22 14:24:59 |
| 84 | AstraZeneca-NGS/disambiguate Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem 27 15 C++ MIT License 2018-05-08 12:07:59 |
| 84 | astrazeneca-cgr-publications/mantis-ml-release mantis-ml: Stochastic semi-supervised learning to prioritise genes from high throughput genomic screens auto-ml, genomics, keras, machine-learning, scikit-learn, tensorflow 27 9 Python Mozilla Public License 2.0 2024-01-26 09:15:43 |
| 84 | bayer-science-for-a-better-life/data2text-bioleaflets Biomedical Data-to-Text Generation via Fine-Tuning Transformers biomedical-text-mining, data-to-text, nlp-machine-learning, transformers 27 3 Python Apache License 2.0 2021-12-20 10:49:50 |
| 84 | Novartis/easyTrackHubs This package provides a function to reformat lists of genome coverage files, such as bigWig of bam files, into the directory structure of a UCSC Track Hub ready to be visualized in the genome browser. For details about it's use, please have a look at the vignette of the package. 27 HTML GNU General Public License v3.0 2024-04-29 14:38:30 |
| 84 | Novartis/ChemBioMultimodalAutoencoders a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures 27 3 Python MIT License 2023-07-05 14:07:40 |
| 84 | insightsengineering/random.cdisc.data Create random CDISC data cdisc, dataset, r 27 5 R Other 2024-05-24 00:54:03 |
| 85 | Merck/Line-of-Therapy-Algorithm This is the Line of Therapy Algorithm, as described in the paper "Temporal phenotyping by mining healthcare data to derive lines of therapy for cancer" pending submission in the Journal of Biomedical Informatics. 26 14 Python GNU General Public License v3.0 2024-04-29 14:14:27 |
| 85 | rdkit/neo4j-rdkit 26 5 Java BSD 2-Clause "Simplified" License 2023-03-09 18:52:14 |
| 85 | 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 |
| 85 | rgcgithub/clamms CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data. 26 10 C Other 2021-02-20 09:05:58 |
| 86 | MolecularAI/DockStreamCommunityastrazeneca, chemoinformatics, denovo-design, jupyter-notebook, molecular-docking, reinforcement-learning 25 12 Jupyter Notebook Apache License 2.0 2023-03-16 07:06:23 |
| 87 | MolecularAI/maize A graph-based workflow manager for computational chemistry pipelines 24 1 Python Apache License 2.0 2024-01-23 16:42:58 |
| 87 | Bayer-Group/cellenium Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing). bioinformatics, dataviz, scrna-seq, transcriptomics 24 5 Jupyter Notebook MIT License 2023-11-22 11:49:19 |
| 87 | bayer-science-for-a-better-life/pKAI pKAI: a fast and interpretable deep learning approach to accurate electrostatics-driven pKa prediction 24 6 Python MIT License 2021-09-16 09:48:09 |
| 87 | bayer-science-for-a-better-life/neuraldecipher Implementation of the paper "Neuraldecipher - Reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures" by Tuan Le, Robin Winter, Frank Noé and Djork-Arné Clevert computational-chemistry, deep-learning, extended-connectivity-fingerprints, representation-learning, smiles 24 9 Python GNU General Public License v3.0 2020-10-01 14:33:21 |
| 87 | GSK-Biostatistics/neointerface NeoInterface - Neo4j made easy for Python programmers! database, graph-database, neo4j, python 24 5 Python Apache License 2.0 2024-03-20 08:38:11 |
| 87 | Merck/sonar-r-plugin Adds support for R language into SonarQube. It uses output from lintr tool which is processed by the plugin and uploaded into SonarQube server. rlanguage, sonarqube 24 18 Java Apache License 2.0 2024-03-04 22:33:44 |
| 87 | Novartis/xgx Exploratory Graphics for PKPD data 24 8 HTML 2023-10-13 20:07:57 |
| 87 | rdkit/knime-rdkit The RDKit nodes for the KNIME Analytics Platform 24 14 Java 2024-03-11 16:54:55 |
| 87 | biosustain/croissance Tool for estimating growth rates from microbial growth curves bioinformatics, biology, curve-fitting, growth-curves 24 11 Python Other 2021-08-09 11:56:01 |
| 87 | genentech/polygraph Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements. 24 Jupyter Notebook MIT License 2024-04-11 21:51:25 |
| 88 | AbbVie-ComputationalGenomics/genetic-evidence-approvaldrug-target-prioritization, genetic-associations 23 11 R Apache License 2.0 2021-01-14 18:06:50 |
| 88 | AstraZeneca/Omicsfold Multi-omics data normalisation, model fitting and visualisation. 23 7 R Apache License 2.0 2023-04-06 15:01:06 |
| 88 | rdkit/PREFER 23 3 Python BSD 3-Clause "New" or "Revised" License 2023-07-28 07:25:31 |
| 88 | rdkit/benchmarking_platform 23 20 Python 2022-12-19 16:47:27 |
| 88 | 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 |
| 88 | bioinform/breakseq2 BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants 23 5 Python BSD 2-Clause "Simplified" License 2016-03-17 21:03:54 |
| 88 | pfizer-opensource/bigwig-loader A fast dataloader for bigwig files made for machine learning 23 1 Python Apache License 2.0 2024-04-15 13:26:29 |
| 89 | MolecularAI/reinvent-hitl Code for paper "Human-in-the-Loop Assisted de Novo Molecular Design". 22 5 Python Apache License 2.0 2023-03-17 15:13:20 |
| 89 | astrazeneca-cgr-publications/PEACOK Phenome Exome Association and Correlation Of Key phenotypes 22 4 R GNU General Public License v3.0 2021-08-19 16:57:33 |
| 89 | Bayer-Group/cf-metrics 22 9 Shell Other 2017-10-23 16:07:20 |
| 89 | Novartis/JAEGER JAEGER is a deep generative approach for small-molecule design 22 6 Python Apache License 2.0 2021-12-21 01:02:17 |
| 89 | rdkit/AutomatedSeriesClassification 22 7 Jupyter Notebook MIT License 2021-06-23 12:33:52 |
| 89 | biosustain/snakemake_UmetaFlow Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake 22 8 Python Apache License 2.0 2024-04-02 11:21:40 |
| 89 | insightsengineering/cards CDISC Analysis Results Data analysis, cdisc, dataset, r 22 R 2024-06-03 15:23:42 |
| 90 | MolecularAI/aizynthtrain Tools to train synthesis prediction models 21 6 Python Apache License 2.0 2024-05-29 14:47:11 |
| 90 | AstraZeneca-NGS/simple_sv_annotation Simplify snpEff annotations for interesting cases 21 4 Python Other 2019-02-18 10:39:43 |
| 90 | astrazeneca-cgr-publications/JARVIS JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes deeplearning, genomics, non-coding-variants, tensorflow, whole-genome-sequencing 21 6 HTML Mozilla Public License 2.0 2023-07-06 21:36:23 |
| 90 | bayer-science-for-a-better-life/topefind-public Finding the pitfalls of deep learning predictors of interacting residues in antibodies 🦠 antibodies, artificial-intelligence, biology, deep-learning, neural-network, protein 21 Python BSD 3-Clause "New" or "Revised" License 2024-02-27 13:48:38 |
| 90 | rdkit/rdkit-orig Older clone of the RDKit subversion repository at http://sourceforge.net/projects/rdkit/ 21 14 C++ Other 2018-07-24 03:08:00 |
| 90 | insightsengineering/rlistings Value formatting and ASCII rendering infrastructure for tables and listings. 21 5 R 2024-06-07 13:34:58 |
| 90 | genentech/covtracer Tools for contextualizing tests, built using covr test traces. 21 4 R Other 2024-01-12 14:26:39 |
| 90 | genentech/dcdfg 21 4 Python Apache License 2.0 2022-10-04 14:06:27 |
| 91 | GSK-Biostatistics/gto gt in officeverse 20 1 R Apache License 2.0 2023-04-14 21:43:52 |
| 91 | Merck/AlgebraicAgents.jl A lightweight framework to enable hierarchical, heterogeneous dynamical systems co-integration. Batteries included! differential-equations, dynamical-systems, julia, julia-language, stochastic-processes 20 3 Julia Other 2024-03-18 14:13:18 |
| 91 | genentech/regLM Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences. 20 Jupyter Notebook MIT License 2024-02-19 04:41:23 |
| 91 | pfizer-opensource/torsional-strain 20 7 Python Apache License 2.0 2023-03-14 13:19:09 |
| 92 | AstraZeneca/VecNER A library of tools for dictionary-based Named Entity Recognition (NER), based on word vector representations to expand dictionary terms. dictionary-based-ner, entity-extraction, natural-language-processing, ner, nlp 19 Python Apache License 2.0 2023-07-25 21:03:18 |
| 92 | MolecularAI/route-distances Tools and routines to calculate distances between synthesis routes and to cluster them. astrazeneca, cheminformatics, clustering 19 5 Python MIT License 2024-01-24 14:37:42 |
| 92 | AstraZeneca-Code-Club/beginners-python (forked from: THargreaves/beginners-python) Session material and solutions for the Beginner's Python course at the AstraZeneca Code Club 19 7 8 Jupyter Notebook MIT license 2023-07-20 14:59:39 |
| 92 | Bayer-Group/sas2r Clinical trial data analytic recipes in R for SAS users 19 8 R MIT License 2023-10-26 15:39:46 |
| 92 | Bayer-Group/velocity-dashboard React dashboard component 19 10 JavaScript Other 2019-04-24 21:19:38 |
| 92 | Bayer-Group/aws2scala An idiomatic Scala wrapper of the AWS SDK with both asynchronous and streaming clients. 19 9 Scala 2018-06-08 23:03:36 |
| 92 | Bayer-Group/spray-kamon-metrics Better Kamon metrics for Spray services 19 1 HTML Other 2017-04-26 02:11:43 |
| 92 | Roche/gitlab-stats Gitlab Stats provides more statistics from the GitLab API services 19 1 TypeScript Apache License 2.0 2022-12-05 15:33:32 |
| 93 | 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 |
| 93 | 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 |
| 93 | Novartis/DRUG-seq DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline 18 8 R MIT License 2021-06-10 03:35:35 |
| 93 | Novartis/patprofile Standard patient profile for shiny apps 18 7 R MIT License 2020-04-17 07:58:03 |
| 93 | rdkit/rdkit-structure-renderer JavaScript package for interactive rendering of 2D chemical structures in the browser. 18 2 HTML Other 2024-05-23 17:07:13 |
| 93 | Roche/the-ambassador The Ambassador helps users of coding platforms to create findable, well maintained, properly documented and secure projects. It's purpose is to promote creating Open Source and InnerSource software, that others can rely on. It measures project scores (criticality, activity, scorecard), proactively advises projects. inner-source, innersource, innersource-advisor, open-source, scorecard, scores, software-quality 18 Kotlin Apache License 2.0 2024-05-30 10:56:41 |
| 94 | MolecularAI/Deep-Drug-Coder 17 6 Python MIT License 2023-03-11 12:00:04 |
| 94 | Bayer-Group/pado PAthological Data Obsession - cloud native digital pathology datasets digital-pathology, python 17 2 Python BSD 3-Clause "New" or "Revised" License 2023-03-01 13:46:57 |
| 94 | Bayer-Group/eqgat Research repository for the proposed equivariant graph attention network that operates on large biomolecules proposed by Le et al. (2022) deeplearning, graphneuralnetwork, neural-network, protein-structure 17 Python BSD 3-Clause "New" or "Revised" License 2022-12-01 10:38:45 |
| 94 | Bayer-Group/mwundo GeoJSON object, spray-json formats, and basic Geo/Geometry 17 8 Scala Other 2020-09-17 03:45:35 |
| 94 | Bayer-Group/docker-min-jessie Minimally sized Debian Jessie build 17 7 BSD 3-Clause "New" or "Revised" License 2015-09-30 13:59:00 |
| 94 | Boehringer-Ingelheim/anomaly-detection-in-histology Learning image representations for anomaly detection: application to discovery of histological alterations in drug development anomaly-detection, convolutional-neural-networks, deep-features, deep-learning, drug-toxicity, one-class-classfiation, pytorch 17 1 Python MIT License 2024-01-09 11:40:11 |
| 94 | Merck/ReactiveDynamics.jl A Julia package that implements a category of reaction (transportation) network-type dynamical systems. decision-making, differential-equations, julia-language, optimization, reaction-network, scientific-machine-learning, strategic-planning 17 3 Julia Other 2024-04-23 13:33:18 |
| 94 | Merck/PepSeA 17 9 Python MIT License 2021-10-27 20:27:01 |
| 94 | 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 |
| 94 | genentech/jmpost 17 5 R 2024-06-07 16:30:15 |