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https://github.com/servierhub/top-pharma50

Top open source software from the top 50 pharmaceutical companies
https://github.com/servierhub/top-pharma50
ai awesome awesome-list awesome-lists bioinformatics biology-ai computational-biology computational-chemistry ebiology life-sciences lifescience lifesciences pharma pharmaceuticals servier
Last synced: about 1 month ago
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Top open source software from the top 50 pharmaceutical companies
Host: GitHub
URL: https://github.com/servierhub/top-pharma50
Owner: servierhub
Created: 2024-05-22T00:59:57.000Z (9 months ago)
Default Branch: main
Last Pushed: 2024-06-09T21:18:48.000Z (9 months ago)
Last Synced: 2025-01-16T02:02:27.859Z (about 1 month ago)
Topics: ai, awesome, awesome-list, awesome-lists, bioinformatics, biology-ai, computational-biology, computational-chemistry, ebiology, life-sciences, lifescience, lifesciences, pharma, pharmaceuticals, servier
Language: Makefile
Homepage:
Size: 540 KB
Stars: 54
Watchers: 4
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
Awesome Lists containing this project

top-pharma-fr - **servierhub/top-pharma50** - list`, `awesome-lists`, `bioinformatics`, `biology-ai`, `computational-biology`, `computational-chemistry`, `ebiology`, `life-sciences`, `lifescience`, `lifesciences`, `pharma`, `pharmaceuticals`, `servier`<br><img src='https://github.com/HubTou/topgh/blob/main/icons/gstars.png'> 1 <img src='https://github.com/HubTou/topgh/blob/main/icons/last.png'> 2024-06-01 15:52:09 | (Ranked by starred repositories)
ultimate-awesome - top-pharma50 - Top open source software from the top 50 pharmaceutical companies. (Other Lists / Julia Lists)
README

        

[![Servier Contributed](https://raw.githubusercontent.com/servierhub/.github/main/badges/contributed.svg)](https://github.com/ServierHub/)

# Top open source software from the top 50 pharmaceutical companies

This is an automatically generated[^1] list of [open source](https://opensource.org/osd) software from the world's [2023 top 50](https://www.pharmexec.com/view/2023-pharm-exec-top-50-companies) [pharmaceutical companies](https://en.wikipedia.org/wiki/List_of_pharmaceutical_companies)[^2] that are present on GitHub.

It will be periodically refreshed from these [GitHub accounts](Results/SOURCES.md) repositories.

You can also access [what they have updated lately](Results/NEW.md)

and [which topics are covered](Results/TOPICS.md) by these software.

## Ranked by starred repositories

> [!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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/MolecularAI/GraphINVENT)
Graph neural networks for molecular design.
 356  74  Python  MIT License  2023-03-11 11:55:32 |

|7|[**MolecularAI/Reinvent**](https://github.com/MolecularAI/Reinvent)
`astrazeneca`, `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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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 |

|14|[**modernatx/seqlike**](https://github.com/modernatx/seqlike)
Unified biological sequence manipulation in Python
`biological-sequences`, `biopython`, `machine-learning`, `sequence`
 202  18  Python  Apache License 2.0  2024-02-16 13:13:05 |

|15|[**rdkit/mmpdb**](https://github.com/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**](https://github.com/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**](https://github.com/MolecularAI/Chemformer)
 188  34  Python  Apache License 2.0  2024-05-29 14:43:33 |

|18|[**AstraZeneca-NGS/VarDict**](https://github.com/AstraZeneca-NGS/VarDict)
VarDict
 186  60  Perl  MIT License  2024-01-05 14:06:13 |

|19|[**AstraZeneca/awesome-drug-discovery-knowledge-graphs**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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/ReinventCommunity**](https://github.com/MolecularAI/ReinventCommunity)
`astrazeneca`, `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**](https://github.com/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**](https://github.com/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|[**johnsonandjohnson/Bodiless-JS**](https://github.com/johnsonandjohnson/Bodiless-JS)
Framework for building editable websites on the JAMStack
 138  59  TypeScript  Apache License 2.0  2024-01-24 03:00:32 |

|26|[**AstraZeneca/SubTab**](https://github.com/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 |

|27|[**AstraZeneca/awesome-shapley-value**](https://github.com/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**](https://github.com/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**](https://github.com/AstraZeneca-NGS/VarDictJava)
VarDict Java port
 127  52  Java  MIT License  2024-01-05 14:03:51 |

|30|[**rdkit/rdkit-js**](https://github.com/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**](https://github.com/Roche/BalancedLossNLP)
 118  23  Jupyter Notebook  Other  2023-06-12 21:51:15 |

|32|[**Merck/deepbgc**](https://github.com/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**](https://github.com/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**](https://github.com/biosustain/cameo)
cameo - computer aided metabolic engineering & optimization
 113  42  Python  Apache License 2.0  2022-11-07 14:54:19 |

|35|[**Merck/Halyard**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/Sanofi-Public/CodonBERT)
Repository for mRNA Paper and CodonBERT publication.
 94  14  Python  Other  2024-05-03 19:24:06 |

|41|[**AstraZeneca/onto_merger**](https://github.com/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**](https://github.com/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|[**bioinform/rnacocktail**](https://github.com/bioinform/rnacocktail)
`rna-seq`
 86  48  Jupyter Notebook  Other  2020-11-11 06:42:10 |

|43|[**AstraZeneca/awesome-drug-pair-scoring**](https://github.com/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 |

|44|[**EliLillyCo/LillyMol**](https://github.com/EliLillyCo/LillyMol)
LillyMol Public Code
 82  29  C++  Apache License 2.0  2024-03-15 21:39:57 |

|45|[**Novartis/YADA**](https://github.com/Novartis/YADA)
Open-source Data Ops
 81  21  Java  Apache License 2.0  2022-11-16 09:27:33 |

|46|[**bioinform/varsim**](https://github.com/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 |

|46|[**AstraZeneca/biology-for-ai**](https://github.com/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**](https://github.com/AstraZeneca-NGS/reference_data)
Reference data: BED files, genes, transcripts, variations.
 78  28  Python  2017-11-28 14:42:42 |

|47|[**Bayer-Group/tiffslide**](https://github.com/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**](https://github.com/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|[**genentech/scimilarity**](https://github.com/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 |

|49|[**Bayer-Group/ol-kit**](https://github.com/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 |

|50|[**insightsengineering/tern**](https://github.com/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 |

|50|[**AstraZeneca/jazzy**](https://github.com/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 |

|51|[**genentech/pviz**](https://github.com/genentech/pviz)
Pviz
 68  22  JavaScript  Other  2016-09-13 06:28:27 |

|52|[**Novartis/peax**](https://github.com/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 |

|52|[**MolecularAI/pysmilesutils**](https://github.com/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 |

|53|[**MolecularAI/PaRoutes**](https://github.com/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|[**Merck/DeepNeuralNet-QSAR**](https://github.com/Merck/DeepNeuralNet-QSAR)
 63  27  Python  GNU General Public License v3.0  2018-10-24 20:07:27 |

|54|[**GSK-Biostatistics/tfrmt**](https://github.com/GSK-Biostatistics/tfrmt)
r package for formatting tables
 63  3  R  Other  2024-04-16 12:52:10 |

|55|[**AstraZeneca/KAZU**](https://github.com/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**](https://github.com/molecularinformatics/Computational-ADME)
 58  13  Python  MIT License  2024-02-15 15:20:55 |

|57|[**pfizer-opensource/scikit-digital-health**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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|[**rdkit/django-rdkit**](https://github.com/rdkit/django-rdkit)
 53  26  Python  BSD 3-Clause "New" or "Revised" License  2024-04-29 21:54:50 |

|60|[**bioinform/metasv**](https://github.com/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 |

|60|[**MolecularAI/Icolos**](https://github.com/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**](https://github.com/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 |

|61|[**Novartis/cellxgene-gateway**](https://github.com/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|[**rdkit/UGM_2020**](https://github.com/rdkit/UGM_2020)
Materials from the (virtual) 2020 RDKit UGM
 51  22  Jupyter Notebook  2020-10-26 03:39:26 |

|62|[**Merck/matcher**](https://github.com/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|[**genentech/sVAE**](https://github.com/genentech/sVAE)
 51  5  Python  Apache License 2.0  2023-07-21 14:07:07 |

|62|[**MolecularAI/QSARtuna**](https://github.com/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**](https://github.com/MolecularAI/Lib-INVENT)
 51  30  Jupyter Notebook  Apache License 2.0  2023-03-11 11:39:46 |

|63|[**Boehringer-Ingelheim/pyPept**](https://github.com/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|[**rdkit/conda-rdkit**](https://github.com/rdkit/conda-rdkit)
Conda build recipe for the rdkit
 49  30  C  2022-01-11 05:44:22 |

|64|[**Bayer-Group/stax**](https://github.com/Bayer-Group/stax)
AWS CloudFormation stack manager
 49  8  Shell  Other  2015-08-31 18:03:41 |

|65|[**Roche/gitlab-configuration-as-code**](https://github.com/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|[**genentech/walk-jump**](https://github.com/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 |

|66|[**EliLillyCo/pytest-wdl**](https://github.com/EliLillyCo/pytest-wdl)
WDL plugin for pytest
 47  8  Python  Apache License 2.0  2023-08-01 23:14:28 |

|67|[**Merck/rdf2x**](https://github.com/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**](https://github.com/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**](https://github.com/Bayer-Group/column-resizer)
Adds resizable columns to tables
 45  23  JavaScript  Other  2023-10-26 02:34:31 |

|69|[**Novartis/scar**](https://github.com/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**](https://github.com/rdkit/homebrew-rdkit)
Homebrew formula for rdkit
 44  19  Ruby  2022-06-22 08:12:35 |

|69|[**AstraZeneca/skywalkR**](https://github.com/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**](https://github.com/Bayer-Group/stoop)
Monadic Scala API for CouchDB
`beat-not-applicable`
 44  4  Scala  Other  2015-01-13 17:13:53 |

|70|[**Bayer-Group/COLID-Documentation**](https://github.com/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**](https://github.com/rdkit/UGM_2022)
Materials from the 2022 UGM
 42  14  Jupyter Notebook  2022-10-31 16:30:51 |

|72|[**MolecularAI/MolBART**](https://github.com/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|[**johnsonandjohnson/Guppy-iOS**](https://github.com/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|[**rdkit/UGM_2021**](https://github.com/rdkit/UGM_2021)
Materials from the (virtual) 2021 RDKit UGM
 40  18  Jupyter Notebook  2021-10-22 11:44:33 |

|73|[**Merck/Sapiens**](https://github.com/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|[**Bayer-Group/xsmiles**](https://github.com/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 |

|74|[**Novartis/shinyValidator**](https://github.com/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**](https://github.com/Roche/foxops)
Templating for Git Repositories
 39  6  Python  Apache License 2.0  2024-05-27 19:22:11 |

|75|[**AstraZeneca/runnable**](https://github.com/AstraZeneca/runnable)
Runnable
 38  4  Python  Apache License 2.0  2024-06-04 20:42:58 |

|75|[**Bayer-Group/kamon-prometheus**](https://github.com/Bayer-Group/kamon-prometheus)
A Kamon backend to support Prometheus
 38  19  HTML  Other  2017-06-22 19:33:30 |

|76|[**rdkit/shape-it**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/rdkit/UGM_2016)
Materials from the 2016 RDKit UGM
 35  21  Jupyter Notebook  2017-01-09 08:40:28 |

|78|[**Gilead-BioStats/gsm**](https://github.com/Gilead-BioStats/gsm)
Good Statistical Monitoring R Package
 33  8  R  Apache License 2.0  2024-06-06 14:03:31 |

|79|[**pfizer-opensource/TorsionNet**](https://github.com/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 |

|79|[**rdkit/UGM_2023**](https://github.com/rdkit/UGM_2023)
Materials from the 2023 RDKit UGM
 32  15  Jupyter Notebook  2024-01-16 16:04:26 |

|79|[**rdkit/RDKitjs-legacy**](https://github.com/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**](https://github.com/rdkit/CheTo)
CheTo - Chemical Topic Modeling
 32  13  Jupyter Notebook  BSD 3-Clause "New" or "Revised" License  2021-04-12 13:33:39 |

|80|[**insightsengineering/r.pkg.template**](https://github.com/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**](https://github.com/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**](https://github.com/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|[**Novartis/yap**](https://github.com/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**](https://github.com/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 |

|81|[**bayer-science-for-a-better-life/phc-gnn**](https://github.com/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 |

|82|[**Novartis/pQSAR**](https://github.com/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|[**Merck/pkglite**](https://github.com/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|[**insightsengineering/teal.modules.clinical**](https://github.com/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 |

|82|[**AstraZeneca/kgem-in-drug-discovery**](https://github.com/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**](https://github.com/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**](https://github.com/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 |

|83|[**openPfizer/DigitalHealthData**](https://github.com/openPfizer/DigitalHealthData)
Visualization package for Apple Watch data collected by Healthkit
 28  5  Python  Apache License 2.0  2019-04-22 14:24:59 |

|83|[**Novartis/pisces**](https://github.com/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**](https://github.com/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 |

|84|[**Novartis/easyTrackHubs**](https://github.com/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**](https://github.com/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**](https://github.com/insightsengineering/random.cdisc.data)
Create random CDISC data
`cdisc`, `dataset`, `r`
 27  5  R  Other  2024-05-24 00:54:03 |

|84|[**AstraZeneca-NGS/disambiguate**](https://github.com/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**](https://github.com/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**](https://github.com/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 |

|85|[**rdkit/neo4j-rdkit**](https://github.com/rdkit/neo4j-rdkit)
 26  5  Java  BSD 2-Clause "Simplified" License  2023-03-09 18:52:14 |

|85|[**Merck/Line-of-Therapy-Algorithm**](https://github.com/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|[**biosustain/Maud**](https://github.com/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**](https://github.com/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/DockStreamCommunity**](https://github.com/MolecularAI/DockStreamCommunity)
`astrazeneca`, `chemoinformatics`, `denovo-design`, `jupyter-notebook`, `molecular-docking`, `reinforcement-learning`
 25  12  Jupyter Notebook  Apache License 2.0  2023-03-16 07:06:23 |

|87|[**Novartis/xgx**](https://github.com/Novartis/xgx)
Exploratory Graphics for PKPD data
 24  8  HTML  2023-10-13 20:07:57 |

|87|[**rdkit/knime-rdkit**](https://github.com/rdkit/knime-rdkit)
The RDKit nodes for the KNIME Analytics Platform
 24  14  Java  2024-03-11 16:54:55 |

|87|[**Merck/sonar-r-plugin**](https://github.com/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|[**genentech/polygraph**](https://github.com/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 |

|87|[**MolecularAI/maize**](https://github.com/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|[**GSK-Biostatistics/neointerface**](https://github.com/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|[**biosustain/croissance**](https://github.com/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|[**Bayer-Group/cellenium**](https://github.com/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**](https://github.com/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**](https://github.com/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 |

|88|[**pfizer-opensource/bigwig-loader**](https://github.com/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 |

|88|[**AbbVie-ComputationalGenomics/genetic-evidence-approval**](https://github.com/AbbVie-ComputationalGenomics/genetic-evidence-approval)
`drug-target-prioritization`, `genetic-associations`
 23  11  R  Apache License 2.0  2021-01-14 18:06:50 |

|88|[**rdkit/PREFER**](https://github.com/rdkit/PREFER)
 23  3  Python  BSD 3-Clause "New" or "Revised" License  2023-07-28 07:25:31 |

|88|[**rdkit/benchmarking_platform**](https://github.com/rdkit/benchmarking_platform)
 23  20  Python  2022-12-19 16:47:27 |

|88|[**insightsengineering/teal.gallery**](https://github.com/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**](https://github.com/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|[**AstraZeneca/Omicsfold**](https://github.com/AstraZeneca/Omicsfold)
Multi-omics data normalisation, model fitting and visualisation.
 23  7  R  Apache License 2.0  2023-04-06 15:01:06 |

|89|[**Novartis/JAEGER**](https://github.com/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**](https://github.com/rdkit/AutomatedSeriesClassification)
 22  7  Jupyter Notebook  MIT License  2021-06-23 12:33:52 |

|89|[**insightsengineering/cards**](https://github.com/insightsengineering/cards)
CDISC Analysis Results Data
`analysis`, `cdisc`, `dataset`, `r`
 22  R  2024-06-03 15:23:42 |

|89|[**MolecularAI/reinvent-hitl**](https://github.com/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**](https://github.com/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|[**biosustain/snakemake_UmetaFlow**](https://github.com/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|[**Bayer-Group/cf-metrics**](https://github.com/Bayer-Group/cf-metrics)
 22  9  Shell  Other  2017-10-23 16:07:20 |

|90|[**rdkit/rdkit-orig**](https://github.com/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**](https://github.com/insightsengineering/rlistings)
Value formatting and ASCII rendering infrastructure for tables and listings.
 21  5  R  2024-06-07 13:34:58 |

|90|[**genentech/covtracer**](https://github.com/genentech/covtracer)
Tools for contextualizing tests, built using covr test traces.
 21  4  R  Other  2024-01-12 14:26:39 |

|90|[**genentech/dcdfg**](https://github.com/genentech/dcdfg)
 21  4  Python  Apache License 2.0  2022-10-04 14:06:27 |

|90|[**MolecularAI/aizynthtrain**](https://github.com/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**](https://github.com/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**](https://github.com/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**](https://github.com/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 |

|91|[**pfizer-opensource/torsional-strain**](https://github.com/pfizer-opensource/torsional-strain)
 20  7  Python  Apache License 2.0  2023-03-14 13:19:09 |

|91|[**Merck/AlgebraicAgents.jl**](https://github.com/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**](https://github.com/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|[**GSK-Biostatistics/gto**](https://github.com/GSK-Biostatistics/gto)
gt in officeverse
 20  1  R  Apache License 2.0  2023-04-14 21:43:52 |

|92|[**Roche/gitlab-stats**](https://github.com/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 |

|92|[**AstraZeneca/VecNER**](https://github.com/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**](https://github.com/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**](https://github.com/AstraZeneca-Code-Club/beginners-python) (forked from: [THargreaves/beginners-python](https://github.com/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**](https://github.com/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**](https://github.com/Bayer-Group/velocity-dashboard)
React dashboard component
 19  10  JavaScript  Other  2019-04-24 21:19:38 |

|92|[**Bayer-Group/aws2scala**](https://github.com/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**](https://github.com/Bayer-Group/spray-kamon-metrics)
Better Kamon metrics for Spray services
 19  1  HTML  Other  2017-04-26 02:11:43 |

|93|[**Novartis/Causal-inference-in-RCTs**](https://github.com/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**](https://github.com/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**](https://github.com/Novartis/patprofile)
Standard patient profile for shiny apps
 18  7  R  MIT License  2020-04-17 07:58:03 |

|93|[**rdkit/rdkit-structure-renderer**](https://github.com/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**](https://github.com/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 |

|93|[**Bayer-Group/BayerCLAW**](https://github.com/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 |

|94|[**Merck/ReactiveDynamics.jl**](https://github.com/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**](https://github.com/Merck/PepSeA)
 17  9  Python  MIT License  2021-10-27 20:27:01 |

|94|[**insightsengineering/tlg-catalog**](https://github.com/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**](https://github.com/genentech/jmpost)
 17  5  R  2024-06-07 16:30:15 |

|94|[**Roche/neuro-meeglet**](https://github.com/Roche/neuro-meeglet)
Complex-valued Morlet wavelets for EEG signal analysis and feature engineering.
 17  2  Jupyter Notebook  Apache License 2.0  2024-03-29 09:55:14 |

|94|[**MolecularAI/Deep-Drug-Coder**](https://github.com/MolecularAI/Deep-Drug-Coder)
 17  6  Python  MIT License  2023-03-11 12:00:04 |

|94|[**Boehringer-Ingelheim/anomaly-detection-in-histology**](https://github.com/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|[**Bayer-Group/pado**](https://github.com/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**](https://github.com/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 |

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[^1]: This page was generated with the [topgh](https://github.com/HubTou/topgh) open source software on 2024-06-09

[^2]: Independent from other groups