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Servier Contributed

Top open source software from PRISME Forum members

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.

You can also focus on what has been updated lately.

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
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/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
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/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
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/rnacocktail
rna-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/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 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-approval
drug-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

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Footnotes

  1. This page was generated with the topgh open source software on 2024-06-09