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https://github.com/servierhub/top-life-sciences

Top Life Sciences open-source software
https://github.com/servierhub/top-life-sciences
ai awesome awesome-list awesome-lists bioinformatics biology biology-ai computational-biology computational-chemistry ebiology life-sciences lifescience lifesciences pharma pharmaceuticals servier
Last synced: about 1 month ago
JSON representation
Top Life Sciences open-source software
Host: GitHub
URL: https://github.com/servierhub/top-life-sciences
Owner: servierhub
Created: 2024-05-31T22:55:08.000Z (9 months ago)
Default Branch: main
Last Pushed: 2024-06-09T21:14:12.000Z (9 months ago)
Last Synced: 2025-01-08T09:02:38.239Z (about 1 month ago)
Topics: ai, awesome, awesome-list, awesome-lists, bioinformatics, biology, biology-ai, computational-biology, computational-chemistry, ebiology, life-sciences, lifescience, lifesciences, pharma, pharmaceuticals, servier
Language: Makefile
Homepage:
Size: 1.72 MB
Stars: 6
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
Awesome Lists containing this project

top-pharma-fr - **servierhub/top-life-sciences** - source software<br>`ai`, `awesome`, `awesome-list`, `awesome-lists`, `bioinformatics`, `biology`, `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'> 2024-06-06 07:56:59 | (Ranked by starred repositories)
ultimate-awesome - top-life-sciences - Top Life Sciences open-source software. (Other Lists / Julia Lists)
README

        

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

# Top life sciences open source software

This is an automatically generated[^1] **ranked list** of [open source](https://opensource.org/osd) software from

[pharmaceutical companies](https://en.wikipedia.org/wiki/List_of_pharmaceutical_companies) and cross organizations,

[biotechnology companies](https://en.wikipedia.org/wiki/Category:Biotechnology_companies),

research institutes,

open source communities and individuals,

plus some life-science software from technological companies.

It's made from a **curated** list of [GitHub accounts](Results/SOURCES.md), and will be periodically refreshed from these sources' 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|[**google-deepmind/alphafold**](https://github.com/google-deepmind/alphafold)
Open source code for AlphaFold.
 11987  2135  226  Python  Apache-2.0 license  2023-04-05 09:45:53 |

|2|[**deepchem/deepchem**](https://github.com/deepchem/deepchem)
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
`biology`, `deep-learning`, `drug-discovery`, `hacktoberfest`, `materials-science`, `quantum-chemistry`
 5220  1626  Python  MIT License  2024-06-08 13:03:11 |

|3|[**biopython/biopython**](https://github.com/biopython/biopython)
Official git repository for Biopython (originally converted from CVS)
`bioinformatics`, `biopython`, `dna`, `genomics`, `phylogenetics`, `protein`, `protein-structure`, `python`, `sequence-alignment`
 4213  1728  168  Python  Unknown LICENSE |

|4|[**google/deepvariant**](https://github.com/google/deepvariant)
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
`bioinformatics`, `deep-learning`, `deep-neural-network`, `deepvariant`, `dna`, `genome`, `genomics`, `machine-learning`, `ngs`, `science`, `sequencing`, `tensorflow`
 3100  698  159  Python  BSD-3-Clause license  2024-03-19 19:20:10 |

|5|[**facebookresearch/esm**](https://github.com/facebookresearch/esm)
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
 2917  577  63  Python  MIT license  2022-10-18 13:38:47 |

|6|[**aqlaboratory/openfold**](https://github.com/aqlaboratory/openfold)
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
`alphafold2`, `protein-structure`, `pytorch`
 2572  466  Python  Apache License 2.0  2024-06-04 08:33:28 |

|7|[**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 |

|8|[**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 |

|9|[**OpenGene/fastp**](https://github.com/OpenGene/fastp)
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
`adapter`, `bioinformatics`, `duplication`, `fastq`, `filter`, `filtering`, `illumina`, `merging`, `ngs`, `overlap`, `polyg`, `preprocessing`, `qc`, `quality`, `quality-control`, `sequencing`, `splitting`, `trimming`, `umi`
 1803  333  C++  MIT License  2024-04-07 08:16:11 |

|10|[**scverse/scanpy**](https://github.com/scverse/scanpy)
Single-cell analysis in Python. Scales to >1M cells.
`anndata`, `bioinformatics`, `data-science`, `machine-learning`, `python`, `scanpy`, `scverse`, `transcriptomics`, `visualize-data`
 1789  579  Python  BSD 3-Clause "New" or "Revised" License  2024-06-07 08:43:34 |

|11|[**lh3/minimap2**](https://github.com/lh3/minimap2)
A versatile pairwise aligner for genomic and spliced nucleotide sequences
`bioinformatics`, `genomics`, `sequence-alignment`, `spliced-alignment`
 1708  396  C  Other  2024-05-22 19:58:33 |

|12|[**allenai/scispacy**](https://github.com/allenai/scispacy)
A full spaCy pipeline and models for scientific/biomedical documents.
`bioinformatics`, `biomedical`, `custom-pipes`, `nlp`, `scientific-documents`, `spacy`
 1629  221  52  Python  Apache-2.0 license  2024-03-08 05:57:56 |

|13|[**broadinstitute/gatk**](https://github.com/broadinstitute/gatk)
Official code repository for GATK versions 4 and up
`bioinformatics`, `dna`, `gatk`, `genome`, `genomics`, `ngs`, `science`, `sequencing`, `spark`
 1621  577  156  Java  specific  2023-12-13 22:53:56 |

|14|[**bioconda/bioconda-recipes**](https://github.com/bioconda/bioconda-recipes)
Conda recipes for the bioconda channel.
`bioinformatics`, `conda`, `hacktoberfest`, `package-management`
 1595  3089  96  Shell  MIT license |

|15|[**samtools/samtools**](https://github.com/samtools/samtools)
Tools (written in C using htslib) for manipulating next-generation sequencing data
 1572  572  C  Other  2024-06-07 09:32:59 |

|16|[**Slicer/Slicer**](https://github.com/Slicer/Slicer)
Multi-platform, free open source software for visualization and image computing.
`3d-printing`, `3d-slicer`, `c-plus-plus`, `computed-tomography`, `image-guided-therapy`, `image-processing`, `itk`, `kitware`, `medical-image-computing`, `medical-imaging`, `national-institutes-of-health`, `neuroimaging`, `nih`, `python`, `qt`, `registration`, `segmentation`, `tcia-dac`, `tractography`, `vtk`
 1521  520  38  C++  specific |

|17|[**lh3/bwa**](https://github.com/lh3/bwa)
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
`bioinformatics`, `fm-index`, `genomics`, `sequence-alignment`
 1468  547  C  GNU General Public License v3.0  2024-04-15 02:54:32 |

|18|[**DeepGraphLearning/torchdrug**](https://github.com/DeepGraphLearning/torchdrug)
A powerful and flexible machine learning platform for drug discovery
`deep-learning`, `drug-discovery`, `graph-neural-networks`, `pytorch`
 1407  194  31  Python  Apache-2.0 license  2023-07-16 22:37:17 |

|19|[**lh3/seqtk**](https://github.com/lh3/seqtk)
Toolkit for processing sequences in FASTA/Q formats
`bioinformatics`, `sequence-analysis`
 1332  310  C  MIT License  2023-10-24 15:01:39 |

|20|[**galaxyproject/galaxy**](https://github.com/galaxyproject/galaxy)
Data intensive science for everyone.
`bioinformatics`, `dna`, `genomics`, `hacktoberfest`, `ngs`, `pipeline`, `science`, `sequencing`, `usegalaxy`, `workflow`, `workflow-engine`
 1329  967  69  Python  specific  2024-05-07 13:56:26 |

|21|[**schrodinger/fixed-data-table-2**](https://github.com/schrodinger/fixed-data-table-2)
A React table component designed to allow presenting millions of rows of data.
 1290  289  JavaScript  Other  2024-05-23 05:13:10 |

|22|[**soedinglab/MMseqs2**](https://github.com/soedinglab/MMseqs2)
MMseqs2: ultra fast and sensitive search and clustering suite
`alignment`, `bioinformatics`, `blast`, `linclust`, `metagenomics`, `mmseqs`, `profile-search`, `sequence-clustering`, `sequence-search`, `taxonomy`
 1281  181  C  GNU General Public License v3.0  2024-05-23 07:07:21 |

|23|[**facebookresearch/fastMRI**](https://github.com/facebookresearch/fastMRI)
A large-scale dataset of both raw MRI measurements and clinical MRI images.
`convolutional-neural-networks`, `deep-learning`, `fastmri`, `fastmri-challenge`, `fastmri-dataset`, `medical-imaging`, `mri`, `mri-reconstruction`, `pytorch`
 1259  370  74  Python  MIT license  2023-06-26 17:17:06 |

|24|[**greenelab/deep-review**](https://github.com/greenelab/deep-review)
A collaboratively written review paper on deep learning, genomics, and precision medicine
`deep-learning`, `genomics`, `manubot`, `manuscript`, `neural-networks`, `review`
 1235  271  129  HTML  Unknown LICENSE.md  2018-03-12 15:06:48 |

|25|[**shenwei356/seqkit**](https://github.com/shenwei356/seqkit)
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
`bioinformatics`, `cross-platform`, `fasta`, `fastq`, `golang`, `manipulation`, `sequence`, `tool`, `toolkit`
 1226  157  26  Go  MIT license  2024-05-17 15:59:35 |

|26|[**MultiQC/MultiQC**](https://github.com/MultiQC/MultiQC)
Aggregate results from bioinformatics analyses across many samples into a single report.
`analysis`, `bioconda`, `bioinformatics`, `data-visualization`, `multiqc`, `pypi`, `python`, `quality-control`, `reporting`, `seqera`, `vizualisation`
 1185  582  37  JavaScript  GPL-3.0 license  2024-05-31 18:30:12 |

|27|[**dcm4che/dcm4che**](https://github.com/dcm4che/dcm4che)
DICOM Implementation in JAVA
 1165  637  119  Java  specific  2024-04-22 10:59:11 |

|28|[**scverse/scvi-tools**](https://github.com/scverse/scvi-tools)
Deep probabilistic analysis of single-cell and spatial omics data
`cite-seq`, `deep-generative-model`, `deep-learning`, `human-cell-atlas`, `scrna-seq`, `scverse`, `single-cell-genomics`, `single-cell-rna-seq`, `variational-autoencoder`, `variational-bayes`
 1149  342  Python  BSD 3-Clause "New" or "Revised" License  2024-06-05 17:01:13 |

|29|[**vgteam/vg**](https://github.com/vgteam/vg)
tools for working with genome variation graphs
`dna`, `genome-graph`, `genomics`, `graph`, `variation-graph`
 1072  191  48  C++  specific  2024-05-20 18:50:28 |

|30|[**schrodinger/pymol-open-source**](https://github.com/schrodinger/pymol-open-source)
Open-source foundation of the user-sponsored PyMOL molecular visualization system.
 1071  260  C  Other  2024-06-06 19:36:48 |

|31|[**scipipe/scipipe**](https://github.com/scipipe/scipipe)
Robust, flexible and resource-efficient pipelines using Go and the commandline
`bioinformatics`, `bioinformatics-pipeline`, `cheminformatics`, `dataflow`, `fbp`, `go`, `golang`, `pipeline`, `scientific-workflows`, `scipipe`, `workflow`, `workflow-engine`
 1055  72  38  Go  MIT license  2021-10-14 09:11:34 |

|32|[**shenwei356/csvtk**](https://github.com/shenwei356/csvtk)
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
`bioinformatics`, `command-line`, `cross-platform`, `csv`, `golang`, `tool`, `toolkit`, `tsv`
 972  85  25  Go  MIT license  2024-05-29 15:30:38 |

|33|[**bigdatagenomics/adam**](https://github.com/bigdatagenomics/adam)
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
`avro`, `big-data`, `bioinformatics`, `genomics`, `java`, `parquet`, `python`, `r`, `scala`, `spark`
 967  304  Scala  Apache License 2.0  2024-03-23 13:27:52 |

|34|[**broadinstitute/cromwell**](https://github.com/broadinstitute/cromwell)
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
`application`, `bioinformatics`, `cloud`, `containers`, `docker`, `executor`, `ga4gh`, `hpc`, `scala`, `wdl`, `workflow`, `workflow-description-language`, `workflow-execution`
 965  351  112  Scala  BSD-3-Clause LICENSE.txt  2024-05-07 17:47:13 |

|35|[**hail-is/hail**](https://github.com/hail-is/hail)
Cloud-native genomic dataframes and batch computing
`bioinformatics`, `genetics`, `genomics`, `gwas`, `hail`, `python`, `software`, `vcf`
 946  238  55  Python  MIT license  2024-06-05 17:48:05 |

|36|[**broadinstitute/picard**](https://github.com/broadinstitute/picard)
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
 944  365  160  Java  MIT license  2023-11-14 22:01:18 |

|37|[**aqlaboratory/proteinnet**](https://github.com/aqlaboratory/proteinnet)
Standardized data set for machine learning of protein structure
`dataset`, `deep-learning`, `machine-learning`, `protein-sequence`, `protein-structure`, `proteins`
 849  130  Python  MIT License  2020-11-18 23:43:32 |

|38|[**shenwei356/rush**](https://github.com/shenwei356/rush)
A cross-platform command-line tool for executing jobs in parallel
`bioinformatics`, `command`, `cross-platform`, `execute`, `golang`, `parallel`, `pipeline`, `shell`, `windows`
 834  63  20  Go  MIT license  2023-11-13 17:53:58 |

|39|[**evo-design/evo**](https://github.com/evo-design/evo)
DNA foundation modeling from molecular to genome scale
 832  97  Jupyter Notebook  Apache License 2.0  2024-04-30 22:35:34 |

|40|[**PaddlePaddle/PaddleHelix**](https://github.com/PaddlePaddle/PaddleHelix)
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
`biocomputing`, `ddi`, `deeplearning`, `dti`, `graph-networks`, `machine-learning`, `molecule-design`, `ppi`, `protein-design`, `protein-docking`, `protein-folding`, `protein-structure-prediction`, `representation-learning`, `rna-structure-prediction`, `self-supervised-learning`
 799  188  25  Python  Apache-2.0 license  2023-08-01 09:31:36 |

|41|[**samtools/htslib**](https://github.com/samtools/htslib)
C library for high-throughput sequencing data formats
`bam`, `bcf`, `bioinformatics`, `cram`, `htslib`, `ngs`, `sam`, `vcf`
 779  448  C  Other  2024-06-06 15:40:15 |

|42|[**google/nucleus**](https://github.com/google/nucleus)
Python and C++ code for reading and writing genomics data.
`bioinformatics`, `dna`, `genomics`, `tensorflow`
 777  126  53  C++  specific  2021-08-31 23:19:33 |

|43|[**nroduit/Weasis**](https://github.com/nroduit/Weasis)
Weasis is a DICOM viewer available as a desktop application or as a web-based application.
`dicom`, `dicom-image`, `dicom-image-viewer`, `dicom-images`, `dicom-pr`, `dicom-rt`, `dicom-seg`, `dicom-viewer`, `dicom-web-viewer`, `dicomweb`, `ecg`, `export-dicom`, `medical`, `medical-imaging`, `multiplanar-reconstruction`, `viewer`, `volume-rendering`, `weasis`
 763  281  49  Java  specific  2024-05-06 18:42:54 |

|44|[**baidu-research/NCRF**](https://github.com/baidu-research/NCRF)
Cancer metastasis detection with neural conditional random field (NCRF)
`camelyon16`, `conditional-random-fields`, `deep-learning`, `pathology`, `whole-slide-imaging`
 749  184  37  Python  Apache-2.0 license  2018-06-17 18:22:34 |

|45|[**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 |

|46|[**samtools/hts-specs**](https://github.com/samtools/hts-specs)
Specifications of SAM/BAM and related high-throughput sequencing file formats
 627  173  TeX  2024-06-06 06:50:26 |

|47|[**samtools/bcftools**](https://github.com/samtools/bcftools)
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
 626  241  C  Other  2024-06-07 13:13:17 |

|48|[**insilicomedicine/GENTRL**](https://github.com/insilicomedicine/GENTRL)
Generative Tensorial Reinforcement Learning (GENTRL) model
 596  216  Python  2020-04-28 11:58:05 |

|49|[**shenwei356/awesome**](https://github.com/shenwei356/awesome)
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
`awesome`, `data-science`, `git`, `golang`, `linux`, `perl`, `programing-language`, `python`
 593  163  35    MIT license  2023-09-25 02:09:01 |

|50|[**chanzuckerberg/cellxgene**](https://github.com/chanzuckerberg/cellxgene)
An interactive explorer for single-cell transcriptomics data
`dataviz`, `scientific`, `scrna-seq`, `transcriptomics`, `visualization`
 591  111  33  JavaScript  MIT license  2023-12-19 22:19:07 |

|51|[**invesalius/invesalius3**](https://github.com/invesalius/invesalius3)
3D medical imaging reconstruction software
 584  277  37  Python  GPL-2.0 license  2022-04-14 02:28:31 |

|52|[**lh3/bioawk**](https://github.com/lh3/bioawk)
BWK awk modified for biological data
`bioinformatics`, `sequence-analysis`
 582  121  C  2022-08-11 01:06:45 |

|53|[**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 |

|54|[**owkin/PyDESeq2**](https://github.com/owkin/PyDESeq2)
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
`bioinformatics`, `differential-expression`, `python`, `rna-seq`, `transcriptomics`
 533  58  Python  MIT License  2024-06-06 01:43:52 |

|55|[**broadinstitute/infercnv**](https://github.com/broadinstitute/infercnv)
Inferring CNV from Single-Cell RNA-Seq
 520  159  42  R  specific  2020-02-07 20:29:28 |

|56|[**scverse/anndata**](https://github.com/scverse/anndata)
Annotated data.
`anndata`, `bioinformatics`, `data-science`, `machine-learning`, `scanpy`, `scverse`, `transcriptomics`
 511  148  Python  BSD 3-Clause "New" or "Revised" License  2024-06-07 16:03:50 |

|57|[**soedinglab/hh-suite**](https://github.com/soedinglab/hh-suite)
Remote protein homology detection suite.
`alignment`, `bioinformatics`, `cpp`, `hh-suite`, `hhblits`, `hhpred`, `hhsearch`, `opensource`, `profile-profile-search`, `profile-search`, `protein-structure`, `sequence-search`, `simd`, `viterbi`
 509  128  C  GNU General Public License v3.0  2023-08-13 08:44:05 |

|58|[**chhylp123/hifiasm**](https://github.com/chhylp123/hifiasm)
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
`bioinformatics`, `denovo-assembly`, `genomics`, `hifi-read`, `pacbio`
 490  84  28  C++  MIT license  2024-05-06 14:29:45 |

|59|[**insitro/redun**](https://github.com/insitro/redun)
Yet another redundant workflow engine
`aws`, `bioinformatics`, `data-engineering`, `data-science`, `docker`, `etl`, `gcp`, `ml`, `python`, `workflow-engine`
 489  40  Python  Apache License 2.0  2024-06-06 18:52:56 |

|60|[**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 |

|61|[**google-deepmind/alphamissense**](https://github.com/google-deepmind/alphamissense)
 461  58  25  Python  Apache-2.0 license |

|62|[**scverse/squidpy**](https://github.com/scverse/squidpy)
Spatial Single Cell Analysis in Python
`data-visualization`, `image-analysis`, `single-cell-genomics`, `single-cell-rna-seq`, `spatial-analysis`, `spatial-transcriptomics`, `squidpy`
 399  71  Python  BSD 3-Clause "New" or "Revised" License  2024-06-08 21:22:47 |

|63|[**lh3/minigraph**](https://github.com/lh3/minigraph)
Sequence-to-graph mapper and graph generator
`bioinformatics`, `genome-graph`, `genomics`, `pan-genome`, `sequence-alignment`
 394  38  C  MIT License  2024-05-22 00:59:12 |

|64|[**benevolentAI/guacamol**](https://github.com/benevolentAI/guacamol)
Benchmarks for generative chemistry
 383  82  Python  MIT License  2024-02-11 08:59:38 |

|65|[**calico/basenji**](https://github.com/calico/basenji)
Sequential regulatory activity predictions with deep convolutional neural networks.
 373  119  Python  Apache License 2.0  2024-05-28 20:08:23 |

|66|[**ome/bioformats**](https://github.com/ome/bioformats)
Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
`bio-formats`, `format-converter`, `format-reader`, `image`, `java`, `life-sciences-image`, `lightsheet`, `metadata`, `whole-slide-imaging`, `wsi`
 367  239  Java  GNU General Public License v2.0  2024-06-07 19:34:33 |

|67|[**MolecularAI/GraphINVENT**](https://github.com/MolecularAI/GraphINVENT)
Graph neural networks for molecular design.
 356  74  Python  MIT License  2023-03-11 11:55:32 |

|67|[**chembl/chembl_webresource_client**](https://github.com/chembl/chembl_webresource_client)
Official Python client for accessing ChEMBL API
`chembl`, `cheminformatics`, `chemistry`, `chemoinformatics`, `python`, `rest`, `rest-client`
 356  95  Python  Other  2024-02-26 15:44:57 |

|68|[**shenwei356/taxonkit**](https://github.com/shenwei356/taxonkit)
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
`bioinformatics`, `cross-platform`, `lca`, `lineage`, `taxdump`, `taxid`, `taxonkit`, `taxonomy`
 342  29  10  Go  MIT license  2024-04-25 17:15:34 |

|69|[**deepchem/DeepLearningLifeSciences**](https://github.com/deepchem/DeepLearningLifeSciences)
Example code from the book "Deep Learning for the Life Sciences"
 338  150  Jupyter Notebook  MIT License  2021-09-17 05:10:37 |

|70|[**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 |

|71|[**aqlaboratory/rgn**](https://github.com/aqlaboratory/rgn)
Recurrent Geometric Networks for end-to-end differentiable learning of protein structure
`deep-learning`, `deep-neural-networks`, `protein-structure`, `protein-structure-prediction`
 326  89  Python  MIT License  2019-08-01 14:17:59 |

|72|[**tencent-ailab/grover**](https://github.com/tencent-ailab/grover)
This is a Pytorch implementation of the paper: Self-Supervised Graph Transformer on Large-Scale Molecular Data
 313  68  7  Python  specific  2021-01-18 09:06:32 |

|73|[**lh3/miniprot**](https://github.com/lh3/miniprot)
Align proteins to genomes with splicing and frameshift
`bioinformatics`, `sequence-alignment`
 305  16  C  MIT License  2024-04-12 21:01:25 |

|74|[**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 |

|75|[**lh3/miniasm**](https://github.com/lh3/miniasm)
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
`bioinformatics`, `denovo-assembly`, `genomics`
 293  68  TeX  MIT License  2023-12-13 01:35:58 |

|76|[**chanzuckerberg/MedMentions**](https://github.com/chanzuckerberg/MedMentions)
A corpus of Biomedical papers annotated with mentions of UMLS entities.
 291  31  25   |

|77|[**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 |

|78|[**samtools/htsjdk**](https://github.com/samtools/htsjdk)
A Java API for high-throughput sequencing data (HTS) formats.
`bam`, `cram`, `dna`, `fasta`, `genomics`, `java`, `java-api`, `ngs`, `sam`, `sequencing`, `vcf`
 274  244  Java  2024-06-04 18:40:43 |

|79|[**shenwei356/brename**](https://github.com/shenwei356/brename)
A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression
`batch`, `batch-rename`, `batch-rename-files`, `batch-renamer`, `go`, `golang`, `rename`, `safe`, `windows`
 254  21  6  Go  MIT license  2024-04-14 08:22:45 |

|80|[**lh3/wgsim**](https://github.com/lh3/wgsim)
Reads simulator
`bioinformatics`, `genomics`
 252  90  C  2021-09-03 14:58:22 |

|81|[**Acellera/htmd**](https://github.com/Acellera/htmd)
HTMD: Programming Environment for Molecular Discovery
`automate`, `drug-discovery`, `htmd`, `molecular-simulations`
 250  58  Rich Text Format  Other  2024-06-07 15:24:26 |

|82|[**DeepGraphLearning/GearNet**](https://github.com/DeepGraphLearning/GearNet)
GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)
`graph-neural-networks`, `pre-training`, `protein-representation-learning`
 249  26  10  Python  MIT license |

|83|[**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 |

|84|[**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 |

|85|[**insightsengineering/rtables**](https://github.com/insightsengineering/rtables)
Reporting tables with R
`pharmaceuticals`, `r`, `tables`
 213  49  R  Other  2024-06-07 21:27:39 |

|86|[**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 |

|87|[**pharmaverse/admiral**](https://github.com/pharmaverse/admiral)
ADaM in R Asset Library
`cdisc`, `clinical-trials`, `open-source`, `r`
 207  53  R  Apache License 2.0  2024-06-07 18:23:44 |

|87|[**OpenGene/awesome-bio-datasets**](https://github.com/OpenGene/awesome-bio-datasets)
awesome-bio-datasets
 207  42  MIT License  2017-10-28 12:32:15 |

|88|[**OpenGene/AfterQC**](https://github.com/OpenGene/AfterQC)
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
`adapter-trimming`, `bioinformatics`, `error`, `fastq`, `filtering`, `ngs`, `overlap`, `qc`, `quality-control`, `sequencing`, `trimming`
 203  50  Python  MIT License  2020-05-14 07:15:54 |

|89|[**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 |

|89|[**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 |

|89|[**scverse/scirpy**](https://github.com/scverse/scirpy)
A scanpy extension to analyse single-cell TCR and BCR data.
 202  31  Python  BSD 3-Clause "New" or "Revised" License  2024-06-06 06:21:35 |

|90|[**lh3/gfatools**](https://github.com/lh3/gfatools)
Tools for manipulating sequence graphs in the GFA and rGFA formats
`bioinformatics`, `genome-graph`, `genomics`
 201  18  C  2024-02-20 15:29:14 |

|90|[**scverse/muon**](https://github.com/scverse/muon)
muon is a multimodal omics Python framework
`anndata`, `cite-seq`, `mudata`, `multi-omics`, `multimodal-data`, `multimodal-omics-analysis`, `muon`, `scanpy`, `scatac-seq`, `scrna-seq`, `scverse`
 201  28  Python  BSD 3-Clause "New" or "Revised" License  2024-05-30 21:21:35 |

|91|[**aws-samples/aws-batch-genomics**](https://github.com/aws-samples/aws-batch-genomics)
Software sets up and runs an genome sequencing analysis workflow using AWS Batch and AWS Step Functions.
 199  75  39  Python  Apache-2.0 license  2018-11-29 18:40:42 |

|92|[**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 |

|93|[**Acellera/moleculekit**](https://github.com/Acellera/moleculekit)
MoleculeKit: Your favorite molecule manipulation kit
`drug-discovery`, `machine-learning`, `molecular-modeling`, `molecular-simulation`, `molecule`, `proteins`
 193  35  Python  Other  2024-06-04 13:53:30 |

|94|[**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 |

|95|[**MolecularAI/Chemformer**](https://github.com/MolecularAI/Chemformer)
 188  34  Python  Apache License 2.0  2024-05-29 14:43:33 |

|96|[**owkin/FLamby**](https://github.com/owkin/FLamby)
Cross-silo Federated Learning playground in Python. Discover 7 real-world federated datasets to test your new FL strategies and try to beat the leaderboard.
`dataset`, `deep-learning`, `differential-privacy`, `federated-learning`, `healthcare`, `machine-learning`, `python`
 187  22  Python  MIT License  2024-06-03 12:18:27 |

|96|[**ome/openmicroscopy**](https://github.com/ome/openmicroscopy)
OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded …
`database`, `image`, `java`, `omero`, `python`, `server`
 187  100  Java  GNU General Public License v2.0  2024-06-08 00:39:30 |

|97|[**AstraZeneca-NGS/VarDict**](https://github.com/AstraZeneca-NGS/VarDict)
VarDict
 186  60  Perl  MIT License  2024-01-05 14:06:13 |

|97|[**scverse/spatialdata**](https://github.com/scverse/spatialdata)
An open and interoperable data framework for spatial omics data
 186  34  Python  BSD 3-Clause "New" or "Revised" License  2024-06-08 00:23:48 |

|98|[**haowenz/chromap**](https://github.com/haowenz/chromap)
Fast alignment and preprocessing of chromatin profiles
`bioinformatics`, `chromatin-profiles`, `genomics`, `sequence-analysis`
 184  18  7  C++  MIT license  2024-02-06 15:29:20 |

|99|[**chao1224/MoleculeSTM**](https://github.com/chao1224/MoleculeSTM)
Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42256-023-00759-6)
`clip`, `computation-chemistry`, `drug-discovery`, `editing`, `foundation-model`, `molecule-editing`, `moleculeclip`, `moleculestm`, `pretraining`, `retrieval`
 182  17  4  Python  specific  2024-04-19 05:25:24 |

|100|[**openpharma/visR**](https://github.com/openpharma/visR)
A package to wrap functionality for plots, tables and diagrams adhering to graphical principles.
 179  32  R  Other  2024-06-04 13:48:59 |

|100|[**chembl/ChEMBL_Structure_Pipeline**](https://github.com/chembl/ChEMBL_Structure_Pipeline)
ChEMBL database structure pipelines
 179  38  Python  MIT License  2023-10-25 15:20:47 |

|101|[**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 |

|102|[**lh3/biofast**](https://github.com/lh3/biofast)
Benchmarking programming languages/implementations for common tasks in Bioinformatics
`bioinformatics`
 175  26  C  2021-12-09 14:10:44 |

|103|[**shenwei356/kmcp**](https://github.com/shenwei356/kmcp)
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
`bigsi`, `cobs`, `fracminhash`, `kmer`, `metagenomics`, `scaled-minhash`, `searching`, `sketch`, `sketching`, `syncmers`, `taxonomic-classification`, `taxonomic-profiling`, `virome`
 173  13  6  Go  MIT license  2023-09-22 04:09:54 |

|104|[**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 |

|105|[**soedinglab/metaeuk**](https://github.com/soedinglab/metaeuk)
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
`bioinformatics`, `eukaryotes`, `gene-discovery`, `gene-prediction`, `metagenomics`
 171  24  C  GNU General Public License v3.0  2024-05-30 09:04:06 |

|106|[**recursionpharma/gflownet**](https://github.com/recursionpharma/gflownet)
GFlowNet library specialized for graph & molecular data
`deep-learning`, `gflownet`, `graph-neural-network`, `pytorch`
 168  34  Python  MIT License  2024-06-06 13:29:06 |

|106|[**scverse/scanpy-tutorials**](https://github.com/scverse/scanpy-tutorials)
Scanpy Tutorials.
 168  113  Jupyter Notebook  2024-06-03 19:42:01 |

|107|[**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 |

|108|[**lh3/readfq**](https://github.com/lh3/readfq)
Fast multi-line FASTA/Q reader in several programming languages
`bioinformatics`, `sequence-analysis`
 166  60  C  2021-06-06 07:27:15 |

|109|[**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 |

|110|[**lh3/cgranges**](https://github.com/lh3/cgranges)
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
`algorithm`, `bioinformatics`, `genomics`
 161  18  C  MIT License  2024-05-28 21:47:37 |

|110|[**lh3/kmer-cnt**](https://github.com/lh3/kmer-cnt)
Code examples of fast and simple k-mer counters for tutorial purposes
`bioinformatics`, `genomics`, `k-mer-counting`
 161  13  C++  MIT License  2020-03-10 16:24:06 |

|111|[**greenelab/tybalt**](https://github.com/greenelab/tybalt)
Training and evaluating a variational autoencoder for pan-cancer gene expression data
`analysis`, `autoencoder`, `cancer`, `cancer-genomics`, `deep-learning`, `gene-expression`, `script`, `tool`, `unsupervised-learning`, `variational-autoencoder`, `variational-autoencoders`
 159  62  10  HTML  BSD-3-Clause license  2017-11-13 13:38:42 |

|112|[**aqlaboratory/genie**](https://github.com/aqlaboratory/genie)
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
`diffusion-models`, `protein-design`
 154  18  Python  Apache License 2.0  2024-04-21 13:48:25 |

|113|[**DeepGraphLearning/ConfGF**](https://github.com/DeepGraphLearning/ConfGF)
Implementation of Learning Gradient Fields for Molecular Conformation Generation (ICML 2021).
 153  34  10  Python  MIT license |

|114|[**benevolentAI/DeeplyTough**](https://github.com/benevolentAI/DeeplyTough)
DeeplyTough: Learning Structural Comparison of Protein Binding Sites
`3d-models`, `deep-learning`, `drug-discovery`, `metric-learning`, `protein-structure`
 151  39  Python  Other  2023-04-07 09:33:44 |

|115|[**chao1224/GraphMVP**](https://github.com/chao1224/GraphMVP)
Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)
`contrastive-learning`, `generative-model`, `geometry`, `graph`, `molecule`, `pretraining`, `self-supervised`, `self-supervised-learning`
 150  20  5  Python  MIT license  2022-09-20 14:29:48 |

|116|[**OpenGene/MutScan**](https://github.com/OpenGene/MutScan)
Detect and visualize target mutations by scanning FastQ files directly
`bioinformatics`, `cancer`, `detection`, `fastq`, `mutation`, `ngs`, `somatic`, `validation`, `variant`, `visualization`
 146  38  C  MIT License  2022-02-10 01:52:44 |

|117|[**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 |

|117|[**lh3/psmc**](https://github.com/lh3/psmc)
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
`bioinformatics`, `genomics`, `population-genetics`
 145  60  C  Other  2022-11-21 04:39:31 |

|117|[**tencent-ailab/DrugOOD**](https://github.com/tencent-ailab/DrugOOD)
OOD Dataset Curator and Benchmark for AI-aided Drug Discovery
 145  19  6  Python  specific |

|118|[**ome/ome-zarr-py**](https://github.com/ome/ome-zarr-py)
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
`ngff`, `ome`, `ome-zarr`, `zarr`
 143  51  Python  Other  2024-06-06 12:51:57 |

|119|[**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 |

|120|[**aws-samples/aws-genomics-workflows**](https://github.com/aws-samples/aws-genomics-workflows)
Genomics Workflows on AWS
`aws`, `batch`, `genomics`, `step-functions`, `workflows`
 140  106  19  Shell  MIT-0 license  2022-03-30 21:38:09 |

|121|[**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 |

|122|[**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 |

|122|[**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 |

|123|[**Benson-Genomics-Lab/TRF**](https://github.com/Benson-Genomics-Lab/TRF)
Tandem Repeats Finder: a program to analyze DNA sequences
 137  24  C  GNU Affero General Public License v3.0  2023-01-16 20:44:26 |

|124|[**lh3/pangene**](https://github.com/lh3/pangene)
Constructing a pangenome gene graph
`bioinformatics`, `pangenome`
 136  7  C  2024-05-29 00:13:01 |

|125|[**owkin/HistoSSLscaling**](https://github.com/owkin/HistoSSLscaling)
Code associated to the publication: Scaling self-supervised learning for histopathology with masked image modeling, A. Filiot et al., MedRxiv (2023). We publicly release Phikon 🚀
`computational-pathology`
 135  11  Jupyter Notebook  Other  2024-01-29 22:35:32 |

|126|[**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 |

|127|[**lh3/bedtk**](https://github.com/lh3/bedtk)
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
`bioinformatics`
 132  15  C  MIT License  2024-05-28 21:48:28 |

|128|[**Bioconductor/Contributions**](https://github.com/Bioconductor/Contributions)
Contribute Packages to Bioconductor
`bioconductor`
 131  33  2023-09-12 18:32:10 |

|129|[**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 |

|129|[**soedinglab/plass**](https://github.com/soedinglab/plass)
sensitive and precise assembly of short sequencing reads
`bioinformatics`, `metagenomics`, `metatranscriptomics`, `opensource`, `proteins`, `proteomics`, `sequence-assembler`
 129  14  C  GNU General Public License v3.0  2024-04-16 20:44:12 |

|130|[**benevolentAI/guacamol_baselines**](https://github.com/benevolentAI/guacamol_baselines)
Baselines models for GuacaMol benchmarks
 128  33  Python  MIT License  2024-02-16 09:40:42 |

|131|[**AstraZeneca-NGS/VarDictJava**](https://github.com/AstraZeneca-NGS/VarDictJava)
VarDict Java port
 127  52  Java  MIT License  2024-01-05 14:03:51 |

|132|[**lh3/ksw2**](https://github.com/lh3/ksw2)
Global alignment and alignment extension
`bioinformatics`, `sequence-alignment`
 124  24  C  Other  2023-06-27 17:21:12 |

|132|[**chao1224/ChatDrug**](https://github.com/chao1224/ChatDrug)
LLM for Drug Editing, ICLR 2024
`chatgpt`, `chatgpt3`, `conversation`, `domain-feedback`, `drug`, `drug-discovery`, `drug-editing`, `editing`, `llm`, `molecule`, `motif`, `peptide`, `protein`, `retrieval`, `secondary-structure`, `small-molecule`, `structure`
 124  8  3  Python  2024-05-28 19:44:44 |

|133|[**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 |

|133|[**blazerye/DrugAssist**](https://github.com/blazerye/DrugAssist)
DrugAssist: A Large Language Model for Molecule Optimization
`ai-for-science`, `drug-discovery`, `instruction-datasets`, `instruction-tuning`, `large-language-models`, `molecule-generation`, `molecule-optimization`
 123  10  3  Python |

|134|[**bigdatagenomics/mango**](https://github.com/bigdatagenomics/mango)
A scalable genome browser. Apache 2 licensed.
 122  30  Scala  Apache License 2.0  2022-12-02 22:21:57 |

|135|[**OpenGene/repaq**](https://github.com/OpenGene/repaq)
A fast lossless FASTQ compressor with ultra-high compression ratio
 120  20  C  MIT License  2023-09-22 02:48:34 |

|136|[**Bioconductor/BiocStickers**](https://github.com/Bioconductor/BiocStickers)
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
`bioconductor`, `stickers`
 119  86  R  Other  2024-05-10 05:58:21 |

|136|[**greenelab/pancancer**](https://github.com/greenelab/pancancer)
Building classifiers using cancer transcriptomes across 33 different cancer-types
`analysis`, `cancer`, `classifier`, `gene-expression`, `machine-learning`, `methodology`, `pancancer`, `tcga`, `tool`, `transcriptome`
 119  58  10  Jupyter Notebook  BSD-3-Clause license  2018-03-01 15:38:33 |

|137|[**Roche/BalancedLossNLP**](https://github.com/Roche/BalancedLossNLP)
 118  23  Jupyter Notebook  Other  2023-06-12 21:51:15 |

|138|[**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 |

|138|[**benevolentAI/MolBERT**](https://github.com/benevolentAI/MolBERT)
 117  35  Python  MIT License  2021-06-06 10:28:35 |

|139|[**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 |

|140|[**OpenGene/GeneFuse**](https://github.com/OpenGene/GeneFuse)
Gene fusion detection and visualization
`alk`, `bioinformatics`, `cancer`, `cosmic`, `eml4`, `fusion`, `gene`, `ret`, `ros1`
 114  62  C  MIT License  2022-02-21 08:07:06 |

|141|[**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 |

|142|[**EBI-Metagenomics/emg-viral-pipeline**](https://github.com/EBI-Metagenomics/emg-viral-pipeline)
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
`cwl`, `nextflow`, `pipeline`, `viruses`, `workflow`
 109  13  Python  Apache License 2.0  2024-05-08 20:10:03 |

|142|[**OpenGene/gencore**](https://github.com/OpenGene/gencore)
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
`bioinformatics`, `consensus`, `deduplication`, `deep-sequencing`, `duplex`, `duplex-sequencing`, `duplication`, `ngs`, `sequencing`, `sequencing-error`, `sequencing-noise`, `somatic`
 109  32  C++  MIT License  2023-10-27 06:19:21 |

|142|[**OpenGene/fastv**](https://github.com/OpenGene/fastv)
An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
`2019-ncov`, `bioinformatics`, `coronavirus`, `covid`, `covid-19`, `hcov`, `meta-genomics`, `microbial-sequences`, `mngs`, `ngs`, `sars-cov-2`, `sequencing`, `viral`, `viral-infectious-diseases`, `virus`, `visualization`
 109  24  C++  MIT License  2023-10-27 06:16:38 |

|143|[**lh3/yak**](https://github.com/lh3/yak)
Yet another k-mer analyzer
`bioinformatics`, `k-mer`
 108  8  C  MIT License  2024-04-01 21:39:44 |

|143|[**lh3/fermikit**](https://github.com/lh3/fermikit)
De novo assembly based variant calling pipeline for Illumina short reads
`bioinformatics`, `denovo-assembly`, `genomics`, `variant-calling`
 108  23  TeX  Other  2020-11-30 22:57:56 |

|144|[**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 |

|144|[**ome/ngff**](https://github.com/ome/ngff)
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
`bioimaging`, `cloud`, `data-science`, `file-formats`, `spec`
 107  38  Bikeshed  Other  2024-06-02 06:26:47 |

|144|[**soedinglab/CCMpred**](https://github.com/soedinglab/CCMpred)
Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
 107  25  C  GNU Affero General Public License v3.0  2023-11-08 07:51:35 |

|145|[**lh3/minimap**](https://github.com/lh3/minimap)
This repo is DEPRECATED. Please use minimap2, the successor of minimap.
 106  29  C  MIT License  2017-09-20 14:15:02 |

|146|[**chao1224/Geom3D**](https://github.com/chao1224/Geom3D)
Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023
`3d`, `3d-structures`, `ai4science`, `biology`, `chemistry`, `crystals`, `drugs`, `equivariance`, `geometry`, `group`, `invariance`, `material`, `molecules`, `physics`, `proteins`, `symmetry`
 105  9  2  Python  MIT license  2024-06-05 03:18:58 |

|147|[**phuse-org/phuse-scripts**](https://github.com/phuse-org/phuse-scripts)
Delivery standard industry analyses, built upon CDISC standards for analysis data
 104  88  SAS  MIT License  2023-08-01 15:21:20 |

|147|[**chembl/FPSim2**](https://github.com/chembl/FPSim2)
Simple package for fast molecular similarity searches
`cheminformatics`, `chemistry`, `gpu`, `python`, `similarity-search`
 104  17  Python  MIT License  2024-02-15 11:13:05 |

|148|[**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 |

|149|[**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 |

|150|[**openpharma/mmrm**](https://github.com/openpharma/mmrm)
Mixed Models for Repeated Measures (MMRM) in R.
 100  17  R  Other  2024-06-03 18:02:15 |

|150|[**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 |

|150|[**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 |

|151|[**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 |

|152|[**lh3/hickit**](https://github.com/lh3/hickit)
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
`bioinformatics`, `genomics`, `hi-c`
 98  11  C  2021-02-04 01:47:43 |

|153|[**aqlaboratory/rgn2**](https://github.com/aqlaboratory/rgn2)
 97  28  Python  2023-11-28 17:16:23 |

|154|[**lh3/bgt**](https://github.com/lh3/bgt)
Flexible genotype query among 30,000+ samples whole-genome
`bioinformatics`, `genomics`
 96  10  C  MIT License  2019-09-04 19:43:27 |

|154|[**scverse/rapids_singlecell**](https://github.com/scverse/rapids_singlecell)
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
`anndata`, `bioinformatics`, `gpu`, `scverse`, `single-cell`
 96  18  Python  MIT License  2024-06-03 18:07:06 |

|154|[**shenwei356/bio_scripts**](https://github.com/shenwei356/bio_scripts)
Practical, reusable scripts for bioinformatics
`bioinformatics`, `perl`, `python`, `reusable`, `script`
 96  65  Perl  MIT License  2019-02-12 13:21:47 |

|155|[**EBISPOT/OLS**](https://github.com/EBISPOT/OLS)
Ontology Lookup Service from SPOT at EBI
`java`, `neo4j`, `obofoundry`, `owl`, `owl-api`
 95  40  JavaScript  Apache License 2.0  2023-04-28 20:09:19 |

|156|[**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 |

|156|[**OpenGene/scrnapip**](https://github.com/OpenGene/scrnapip)
A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis
 94  14  HTML  2023-10-16 01:24:06 |

|157|[**EBI-Metagenomics/genomes-catalogue-pipeline**](https://github.com/EBI-Metagenomics/genomes-catalogue-pipeline)
MGnify genome analysis pipeline
 93  21  Python  Other  2024-06-06 09:44:21 |

|158|[**samtools/tabix**](https://github.com/samtools/tabix)
Note: tabix and bgzip binaries are now part of the HTSlib project.
 92  40  C  2021-08-03 14:29:38 |

|158|[**shenwei356/BlackheartedHospital**](https://github.com/shenwei356/BlackheartedHospital) (forked from: [open-power-workgroup/Hospital](https://github.com/open-power-workgroup/Hospital))
网传附莆田系医院名单，欢迎更新
 92  15  2016-05-03 07:06:09 |

|159|[**AbSciBio/unlocking-de-novo-antibody-design**](https://github.com/AbSciBio/unlocking-de-novo-antibody-design)
 91  14  Other  2024-01-09 17:36:19 |

|159|[**schrodinger/gpusimilarity**](https://github.com/schrodinger/gpusimilarity)
A Cuda/Thrust implementation of fingerprint similarity searching
`cheminformatics`, `chemistry`, `gpu`, `similarity-analysis`
 91  26  C++  BSD 3-Clause "New" or "Revised" License  2024-01-24 19:08:08 |

|159|[**lh3/dipcall**](https://github.com/lh3/dipcall)
Reference-based variant calling pipeline for a pair of phased haplotype assemblies
 91  9  JavaScript  MIT License  2021-06-06 20:36:10 |

|160|[**Bioconductor/CSAMA**](https://github.com/Bioconductor/CSAMA)
Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology
 89  45  HTML  2024-06-06 12:04:08 |

|160|[**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 |

|160|[**hoelzer-lab/rnaflow**](https://github.com/hoelzer-lab/rnaflow)
A simple RNA-Seq differential gene expression pipeline using Nextflow
 89  19  HTML  GNU General Public License v3.0  2024-02-26 20:45:37 |

|160|[**shenwei356/perfect-bioinformatic-tools**](https://github.com/shenwei356/perfect-bioinformatic-tools)
What should perfect bioinformatic tools be like?
`bioinformatics`, `cli`, `usability`
 89  1  Creative Commons Zero v1.0 Universal  2024-03-19 10:22:54 |

|161|[**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 |

|161|[**calico/scBasset**](https://github.com/calico/scBasset)
Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
 88  11  Jupyter Notebook  Apache License 2.0  2024-02-08 19:20:16 |

|161|[**shenwei356/bio**](https://github.com/shenwei356/bio)
A lightweight and high-performance bioinformatics package in Golang
`bioinformatics`, `golang`, `minimizer`, `package`, `scaled-minhash`, `sequence`, `syncmer`, `taxdump`, `taxonomy`
 88  9  7  Go  MIT license  2024-03-11 09:41:44 |

|162|[**owkin/HE2RNA_code**](https://github.com/owkin/HE2RNA_code)
Train a model to predict gene expression from histology slides.
 87  39  Python  GNU General Public License v3.0  2022-07-06 20:53:24 |

|162|[**scverse/pertpy**](https://github.com/scverse/pertpy)
Perturbation Analysis in the scverse ecosystem.
`perturbation`, `scverse`, `single-cell`
 87  19  Python  MIT License  2024-06-08 08:07:34 |

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