This is an automatically generated1 list of open source software from the world's 2023 top 50 pharmaceutical companies2 that are present on GitHub. It will be periodically refreshed from these GitHub accounts 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 |
---|---|
1 | rdkit/rdkit The official sources for the RDKit library c-plus-plus , cheminformatics , python , rdkit ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
4 | MolecularAI/aizynthfinder A tool for retrosynthetic planning astrazeneca , chemical-reactions , cheminformatics , monte-carlo-tree-search , neural-networks , reaction-informatics ![]() ![]() ![]() ![]() ![]() |
5 | biosustain/potion Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine flask , flask-extensions , mongoengine , peewee , sqlalchemy ![]() ![]() ![]() ![]() ![]() |
6 | MolecularAI/GraphINVENT Graph neural networks for molecular design. ![]() ![]() ![]() ![]() ![]() |
7 | MolecularAI/Reinventastrazeneca , cheminformatics , denovo-design , neural-networks , reinforcement-learning , transfer-learning ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
11 | rdkit/rdkit-tutorials Tutorials to learn how to work with the RDKit ![]() ![]() ![]() ![]() ![]() |
12 | insightsengineering/rtables Reporting tables with R pharmaceuticals , r , tables ![]() ![]() ![]() ![]() ![]() |
13 | Bayer-Group/cloudformation-template-generator A type-safe Scala DSL for generating CloudFormation templates ![]() ![]() ![]() ![]() ![]() |
14 | Bayer-Group/etcd-aws-cluster A container to assist in managing a etcd2 cluster from an Amazon auto scaling group ![]() ![]() ![]() ![]() ![]() |
14 | modernatx/seqlike Unified biological sequence manipulation in Python biological-sequences , biopython , machine-learning , sequence ![]() ![]() ![]() ![]() ![]() |
15 | rdkit/mmpdb A package to identify matched molecular pairs and use them to predict property changes. ![]() ![]() ![]() ![]() ![]() |
16 | bioinform/somaticseq An ensemble approach to accurately detect somatic mutations using SomaticSeq cancer-genomics , somatic-variants ![]() ![]() ![]() ![]() ![]() |
17 | MolecularAI/Chemformer![]() ![]() ![]() ![]() ![]() |
18 | AstraZeneca-NGS/VarDict VarDict ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
20 | rgcgithub/regenie regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. ![]() ![]() ![]() ![]() ![]() |
21 | bioinform/neusomatic NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection convolutional-neural-networks , deep-learning , genomics , somatic-variants ![]() ![]() ![]() ![]() ![]() |
22 | insightsengineering/teal Exploratory Web Apps for Analyzing Clinical Trial Data clinical-trials , nest , r , shiny , webapp ![]() ![]() ![]() ![]() ![]() |
23 | MolecularAI/ReinventCommunityastrazeneca , cheminformatics , denovo-design , jupyter-notebook , neural-networks , reinforcement-learning , transfer-learning ![]() ![]() ![]() ![]() ![]() |
24 | Novartis/tidymodules An Object-Oriented approach to Shiny modules communication , inheritance , oop , r , shiny , shiny-modules , tidy-operators ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
26 | johnsonandjohnson/Bodiless-JS Framework for building editable websites on the JAMStack ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
29 | AstraZeneca-NGS/VarDictJava VarDict Java port ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
31 | Roche/BalancedLossNLP![]() ![]() ![]() ![]() ![]() |
32 | Merck/deepbgc BGC Detection and Classification Using Deep Learning bidirectional-lstm , biosynthetic-gene-clusters , deep-learning , deepbgc , natural-products , pfam2vec , python , synthetic-biology ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
34 | biosustain/cameo cameo - computer aided metabolic engineering & optimization ![]() ![]() ![]() ![]() ![]() |
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. ![]() ![]() ![]() ![]() ![]() |
36 | bayer-science-for-a-better-life/Img2Mol![]() ![]() ![]() ![]() ![]() |
37 | Biogen-Inc/tidyCDISC Demo the app here: https://bit.ly/tidyCDISC_app pharma , r , rinpharma , rstats ![]() ![]() ![]() ![]() ![]() |
38 | MolecularAI/DockStream DockStream: A Docking Wrapper to Enhance De Novo Molecular Design astrazeneca , chemoinformatics , denovo-design , jupyter-notebook , molecular-docking , reinforcement-learning ![]() ![]() ![]() ![]() ![]() |
38 | Bayer-Group/paquo PAthological QUpath Obsession - QuPath and Python conversations digital-pathology , python , qupath ![]() ![]() ![]() ![]() ![]() |
39 | genentech/gReLU gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences. ![]() ![]() ![]() ![]() ![]() |
40 | Sanofi-Public/CodonBERT Repository for mRNA Paper and CodonBERT publication. ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
42 | Sanofi-IADC/whispr Open source event, comment and alert processing hub created by Sanofi IADC ![]() ![]() ![]() ![]() ![]() |
43 | bioinform/rnacocktailrna-seq ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
44 | EliLillyCo/LillyMol LillyMol Public Code ![]() ![]() ![]() ![]() ![]() |
45 | Novartis/YADA Open-source Data Ops ![]() ![]() ![]() ![]() ![]() |
46 | bioinform/varsim VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications genomics , high-throughput-sequencing , simulation , validation ![]() ![]() ![]() ![]() ![]() |
46 | AstraZeneca/biology-for-ai learning biology syllabus, geared for machine learning folks ![]() ![]() ![]() |
46 | AstraZeneca-NGS/reference_data Reference data: BED files, genes, transcripts, variations. ![]() ![]() ![]() ![]() |
47 | Bayer-Group/tiffslide TiffSlide - cloud native openslide-python replacement based on tifffile digital-pathology , python ![]() ![]() ![]() ![]() ![]() |
48 | Merck/r2rtf Easily Create Production-Ready Rich Text Format (RTF) Table and Figure ![]() ![]() ![]() ![]() ![]() |
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. ![]() ![]() ![]() ![]() ![]() |
49 | Bayer-Group/ol-kit Easy to use, open source React/Openlayers geospatial component toolkit. bayer , components , deprecated , geospatial , maps , openlayers , react , toolkit ![]() ![]() ![]() ![]() ![]() |
50 | insightsengineering/tern Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials clinical-trials , graphs , listings , nest , outputs , r , tables ![]() ![]() ![]() ![]() ![]() |
50 | AstraZeneca/jazzy Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules. ![]() ![]() ![]() ![]() ![]() |
51 | genentech/pviz Pviz ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
52 | MolecularAI/pysmilesutils Utilities for working with SMILES based encodings of molecules for deep learning (PyTorch oriented) ![]() ![]() ![]() ![]() ![]() |
53 | MolecularAI/PaRoutes Home of the PaRoutes framework for benchmarking multi-step retrosynthesis predictions. ![]() ![]() ![]() ![]() ![]() |
54 | Merck/DeepNeuralNet-QSAR![]() ![]() ![]() ![]() ![]() |
54 | GSK-Biostatistics/tfrmt r package for formatting tables ![]() ![]() ![]() ![]() ![]() |
55 | AstraZeneca/KAZU Fast, world class biomedical NER biomedical-text-mining , natural-language-processing , nlp ![]() ![]() ![]() ![]() ![]() |
56 | molecularinformatics/Computational-ADME![]() ![]() ![]() ![]() ![]() |
57 | pfizer-opensource/scikit-digital-health Python package for the processing and analysis of Inertial Measurement Unit Data actigraphy , imu-sensor , python , sensors , wearables ![]() ![]() ![]() ![]() ![]() |
58 | AstraZeneca/kallisto Efficiently calculate 3D-features for quantitative structure-activity relationship approaches. chemistry , computational-chemistry , machinelearning , quantum-chemistry ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
58 | MolecularAI/reaction_utils Utilities for working with datasets of chemical reactions, reaction templates and template extraction. ![]() ![]() ![]() ![]() ![]() |
59 | insightsengineering/thevalidatoR Github Action that generates R Package Validation documentation 🏁 github-actions , r , r-package-automation , validation ![]() ![]() ![]() ![]() ![]() |
60 | rdkit/django-rdkit![]() ![]() ![]() ![]() ![]() |
60 | bioinform/metasv MetaSV: An accurate and integrative structural-variant caller for next generation sequencing ![]() ![]() ![]() ![]() ![]() |
60 | MolecularAI/Icolos Icolos: A workflow manager for structure based post-processing of de novo generated small molecules ![]() ![]() ![]() ![]() ![]() |
60 | Bayer-Group/goldengate-kafka-adapter An adapter for Oracle GoldenGate to push change capture data directly to an Apache Kafka cluster ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
62 | rdkit/UGM_2020 Materials from the (virtual) 2020 RDKit UGM ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
62 | genentech/sVAE![]() ![]() ![]() ![]() ![]() |
62 | MolecularAI/QSARtuna QSARtuna: QSAR model building with the optuna framework compchem , computational-chemistry , hyperparameter-optimization , optuna , qsar , qsar-models , smiles-strings ![]() ![]() ![]() ![]() |
62 | MolecularAI/Lib-INVENT![]() ![]() ![]() ![]() ![]() |
63 | Boehringer-Ingelheim/pyPept pyPept: a python library to generate atomistic 2D and 3D representations of peptides ![]() ![]() ![]() ![]() ![]() |
64 | rdkit/conda-rdkit Conda build recipe for the rdkit ![]() ![]() ![]() ![]() |
64 | Bayer-Group/stax AWS CloudFormation stack manager ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
66 | genentech/walk-jump Official repository for discrete Walk-Jump Sampling (dWJS) antibody , machine-learning , protein-design , protein-sequences , proteins ![]() ![]() ![]() ![]() ![]() |
66 | EliLillyCo/pytest-wdl WDL plugin for pytest ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
67 | bedapub/besca BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis ![]() ![]() ![]() ![]() ![]() |
68 | Bayer-Group/column-resizer Adds resizable columns to tables ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
69 | rdkit/homebrew-rdkit Homebrew formula for rdkit ![]() ![]() ![]() ![]() |
69 | AstraZeneca/skywalkR code for Gogleva et al manuscript drug-discovery , knowledge-graph , recommender-system , shiny-apps , ui ![]() ![]() ![]() ![]() ![]() |
69 | Bayer-Group/stoop Monadic Scala API for CouchDB beat-not-applicable ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
71 | rdkit/UGM_2022 Materials from the 2022 UGM ![]() ![]() ![]() ![]() |
72 | MolecularAI/MolBART Pretrained SMILES transformation model for finetuning for diverse molecular tasks. ![]() ![]() ![]() ![]() ![]() |
73 | johnsonandjohnson/Guppy-iOS iOS pod about a curious fish named Guppy guppy , ios , network-monitoring , networking , swift , urlsession ![]() ![]() ![]() ![]() ![]() |
73 | rdkit/UGM_2021 Materials from the (virtual) 2021 RDKit UGM ![]() ![]() ![]() ![]() |
73 | Merck/Sapiens Sapiens is a human antibody language model based on BERT. antibody , bert , embeddings , language-model , sapiens ![]() ![]() ![]() ![]() ![]() |
73 | Bayer-Group/xsmiles Visualize atom and non-atom attributions and SMILES strings ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
74 | Roche/foxops Templating for Git Repositories ![]() ![]() ![]() ![]() ![]() |
75 | AstraZeneca/runnable Runnable ![]() ![]() ![]() ![]() ![]() |
75 | Bayer-Group/kamon-prometheus A Kamon backend to support Prometheus ![]() ![]() ![]() ![]() ![]() |
76 | rdkit/shape-it Updated version of Silicos-it's shape-based alignment tool ![]() ![]() ![]() ![]() ![]() |
76 | biosustain/shu Multi-dimensional, trans-omics metabolic maps. metabolism , systems-biology , visualization ![]() ![]() ![]() ![]() |
77 | Novartis/torchsurv Deep survival analysis made easy deep-learning , pytorch , survival-analysis ![]() ![]() ![]() ![]() ![]() |
77 | Novartis/ontobrowser OntoBrowser is a web-based application for managing ontologies ![]() ![]() ![]() ![]() ![]() |
77 | rdkit/UGM_2016 Materials from the 2016 RDKit UGM ![]() ![]() ![]() ![]() |
78 | Gilead-BioStats/gsm Good Statistical Monitoring R Package ![]() ![]() ![]() ![]() ![]() |
79 | pfizer-opensource/TorsionNet A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM ![]() ![]() ![]() ![]() ![]() |
79 | rdkit/UGM_2023 Materials from the 2023 RDKit UGM ![]() ![]() ![]() ![]() |
79 | rdkit/RDKitjs-legacy Obsolete codebase, please do not use. ![]() ![]() ![]() ![]() ![]() |
79 | rdkit/CheTo CheTo - Chemical Topic Modeling ![]() ![]() ![]() ![]() ![]() |
80 | insightsengineering/r.pkg.template An opinionated R package template with CI/CD built-in git , github-actions , r , template ![]() ![]() ![]() ![]() ![]() |
80 | Sanofi-IADC/konviw Enterprise public viewer for your Confluence pages cms , confluence , headless-cms , viewer ![]() ![]() ![]() ![]() ![]() |
81 | abbvie-external/OmicNavigator Open-Source Software for Omic Data Analysis and Visualization bioinformatics , genomics , omics , opencpu , r ![]() ![]() ![]() ![]() ![]() |
81 | Novartis/yap High throughput, pain-free big data pipelines. ![]() ![]() ![]() ![]() ![]() |
81 | genentech/iterative-perturb-seq Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
82 | Novartis/pQSAR Massively multitask stacked model for predicting activity of thousands of biological assays ![]() ![]() ![]() ![]() ![]() |
82 | Merck/pkglite Compact Package Representations clinical-trials , ectd , package , packaging-tool , pharmaverse , r ![]() ![]() ![]() ![]() ![]() |
82 | insightsengineering/teal.modules.clinical Provides teal modules for the standard clinical trials outputs clinical-trials , modules , nest , outputs , r , shiny ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
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. ![]() ![]() ![]() ![]() ![]() |
82 | GSK-AI/meta-learning-qsar Meta-Learning GNN Initializations for Low-Resource Molecular Property Prediction ![]() ![]() ![]() ![]() ![]() |
83 | openPfizer/DigitalHealthData Visualization package for Apple Watch data collected by Healthkit ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
83 | Novartis/pqsar2cpd pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules. ![]() ![]() ![]() ![]() ![]() |
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. ![]() ![]() ![]() ![]() |
84 | Novartis/ChemBioMultimodalAutoencoders a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architectures ![]() ![]() ![]() ![]() ![]() |
84 | insightsengineering/random.cdisc.data Create random CDISC data cdisc , dataset , r ![]() ![]() ![]() ![]() ![]() |
84 | AstraZeneca-NGS/disambiguate Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
85 | rdkit/neo4j-rdkit![]() ![]() ![]() ![]() ![]() |
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. ![]() ![]() ![]() ![]() ![]() |
85 | biosustain/Maud Enzyme models that take into account kinetics, allostery and thermodynamics ![]() ![]() ![]() ![]() ![]() |
85 | rgcgithub/clamms CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data. ![]() ![]() ![]() ![]() ![]() |
86 | MolecularAI/DockStreamCommunityastrazeneca , chemoinformatics , denovo-design , jupyter-notebook , molecular-docking , reinforcement-learning ![]() ![]() ![]() ![]() ![]() |
87 | Novartis/xgx Exploratory Graphics for PKPD data ![]() ![]() ![]() ![]() |
87 | rdkit/knime-rdkit The RDKit nodes for the KNIME Analytics Platform ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
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. ![]() ![]() ![]() ![]() |
87 | MolecularAI/maize A graph-based workflow manager for computational chemistry pipelines ![]() ![]() ![]() ![]() ![]() |
87 | GSK-Biostatistics/neointerface NeoInterface - Neo4j made easy for Python programmers! database , graph-database , neo4j , python ![]() ![]() ![]() ![]() ![]() |
87 | biosustain/croissance Tool for estimating growth rates from microbial growth curves bioinformatics , biology , curve-fitting , growth-curves ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
87 | bayer-science-for-a-better-life/pKAI pKAI: a fast and interpretable deep learning approach to accurate electrostatics-driven pKa prediction ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
88 | pfizer-opensource/bigwig-loader A fast dataloader for bigwig files made for machine learning ![]() ![]() ![]() ![]() ![]() |
88 | AbbVie-ComputationalGenomics/genetic-evidence-approvaldrug-target-prioritization , genetic-associations ![]() ![]() ![]() ![]() ![]() |
88 | rdkit/PREFER![]() ![]() ![]() ![]() ![]() |
88 | rdkit/benchmarking_platform![]() ![]() ![]() ![]() |
88 | insightsengineering/teal.gallery A Gallery of Exploratory Web Apps used for Analyzing Clinical Trial Data clinical-trials , nest , r , shiny , webapp ![]() ![]() ![]() ![]() ![]() |
88 | bioinform/breakseq2 BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants ![]() ![]() ![]() ![]() ![]() |
88 | AstraZeneca/Omicsfold Multi-omics data normalisation, model fitting and visualisation. ![]() ![]() ![]() ![]() ![]() |
89 | Novartis/JAEGER JAEGER is a deep generative approach for small-molecule design ![]() ![]() ![]() ![]() ![]() |
89 | rdkit/AutomatedSeriesClassification![]() ![]() ![]() ![]() ![]() |
89 | insightsengineering/cards CDISC Analysis Results Data analysis , cdisc , dataset , r ![]() ![]() ![]() |
89 | MolecularAI/reinvent-hitl Code for paper "Human-in-the-Loop Assisted de Novo Molecular Design". ![]() ![]() ![]() ![]() ![]() |
89 | astrazeneca-cgr-publications/PEACOK Phenome Exome Association and Correlation Of Key phenotypes ![]() ![]() ![]() ![]() ![]() |
89 | biosustain/snakemake_UmetaFlow Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake ![]() ![]() ![]() ![]() ![]() |
89 | Bayer-Group/cf-metrics![]() ![]() ![]() ![]() ![]() |
90 | rdkit/rdkit-orig Older clone of the RDKit subversion repository at http://sourceforge.net/projects/rdkit/ ![]() ![]() ![]() ![]() ![]() |
90 | insightsengineering/rlistings Value formatting and ASCII rendering infrastructure for tables and listings. ![]() ![]() ![]() ![]() |
90 | genentech/covtracer Tools for contextualizing tests, built using covr test traces. ![]() ![]() ![]() ![]() ![]() |
90 | genentech/dcdfg![]() ![]() ![]() ![]() ![]() |
90 | MolecularAI/aizynthtrain Tools to train synthesis prediction models ![]() ![]() ![]() ![]() ![]() |
90 | AstraZeneca-NGS/simple_sv_annotation Simplify snpEff annotations for interesting cases ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
91 | pfizer-opensource/torsional-strain![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
91 | genentech/regLM Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences. ![]() ![]() ![]() ![]() |
91 | GSK-Biostatistics/gto gt in officeverse ![]() ![]() ![]() ![]() ![]() |
92 | Roche/gitlab-stats Gitlab Stats provides more statistics from the GitLab API services ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
92 | MolecularAI/route-distances Tools and routines to calculate distances between synthesis routes and to cluster them. astrazeneca , cheminformatics , clustering ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() ![]() |
92 | Bayer-Group/sas2r Clinical trial data analytic recipes in R for SAS users ![]() ![]() ![]() ![]() ![]() |
92 | Bayer-Group/velocity-dashboard React dashboard component ![]() ![]() ![]() ![]() ![]() |
92 | Bayer-Group/aws2scala An idiomatic Scala wrapper of the AWS SDK with both asynchronous and streaming clients. ![]() ![]() ![]() ![]() |
92 | Bayer-Group/spray-kamon-metrics Better Kamon metrics for Spray services ![]() ![]() ![]() ![]() ![]() |
93 | Novartis/Causal-inference-in-RCTs This repository contains code examples for several methods in a Causal Inference in RCTs short course. ![]() ![]() ![]() ![]() |
93 | Novartis/DRUG-seq DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline ![]() ![]() ![]() ![]() ![]() |
93 | Novartis/patprofile Standard patient profile for shiny apps ![]() ![]() ![]() ![]() ![]() |
93 | rdkit/rdkit-structure-renderer JavaScript package for interactive rendering of 2D chemical structures in the browser. ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |
93 | Bayer-Group/BayerCLAW BayerCLAW workflow orchestration system for AWS aws , bayer-not-classified , bayer-reg-none , beat-not-applicable , pipeline , workflow ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
94 | Merck/PepSeA![]() ![]() ![]() ![]() ![]() |
94 | insightsengineering/tlg-catalog A catalog of Tables, Listings and Graphs (TLGs) created with NEST R packages ![]() ![]() ![]() ![]() ![]() |
94 | genentech/jmpost![]() ![]() ![]() ![]() |
94 | Roche/neuro-meeglet Complex-valued Morlet wavelets for EEG signal analysis and feature engineering. ![]() ![]() ![]() ![]() ![]() |
94 | MolecularAI/Deep-Drug-Coder![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() ![]() |
94 | Bayer-Group/pado PAthological Data Obsession - cloud native digital pathology datasets digital-pathology , python ![]() ![]() ![]() ![]() ![]() |
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 ![]() ![]() ![]() ![]() |