Ranked by starred repositories

• **google-deepmind/alphafold** - 2.0 license 2023-04-05 09:45:53 |
• **deepchem/deepchem** - Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biologybiology, deep-learning, drug-discovery, hacktoberfest, materials-science, quantum-chemistry 5220 1626 Python MIT License 2024-06-08 13:03:11 |
• **biopython/biopython** - structure, python, sequence-alignment` 4213 1728 168 Python Unknown LICENSE |
• **google/deepvariant** - 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 |
• **facebookresearch/esm** - 10-18 13:38:47 |
• **aqlaboratory/openfold** - efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2alphafold2, protein-structure, pytorch 2572 466 Python Apache License 2.0 2024-06-04 08:33:28 |
• **rdkit/rdkit** - plus-plus, cheminformatics, python, rdkit` 2483 845 HTML BSD 3-Clause "New" or "Revised" License 2024-06-08 03:18:22 |
• **AstraZeneca/awesome-explainable-graph-reasoning** - list, deep-learning, explainable-ai, explainable-ml, graph, graph-algorithms, graphml` 1941 129 Apache License 2.0 2022-04-04 14:54:08 |
• **OpenGene/fastp** - 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 |
• **scverse/scanpy** - 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 |
• **lh3/minimap2** - alignment, spliced-alignment` 1708 396 C Other 2024-05-22 19:58:33 |
• **allenai/scispacy** - pipes, nlp, scientific-documents, spacy` 1629 221 52 Python Apache-2.0 license 2024-03-08 05:57:56 |
• **broadinstitute/gatk** - 12-13 22:53:56 |
• **bioconda/bioconda-recipes** - management` 1595 3089 96 Shell MIT license |
• **samtools/samtools** - generation sequencing data 1572 572 C Other 2024-06-07 09:32:59 |
• **Slicer/Slicer** - 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 |
• **lh3/bwa** - 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 |
• **DeepGraphLearning/torchdrug** - learning, drug-discovery, graph-neural-networks, pytorch` 1407 194 31 Python Apache-2.0 license 2023-07-16 22:37:17 |
• **lh3/seqtk** - analysis` 1332 310 C MIT License 2023-10-24 15:01:39 |
• **galaxyproject/galaxy** - engine` 1329 967 69 Python specific 2024-05-07 13:56:26 |
• **schrodinger/fixed-data-table-2** - 05-23 05:13:10 |
• **soedinglab/MMseqs2** - search, sequence-clustering, sequence-search, taxonomy` 1281 181 C GNU General Public License v3.0 2024-05-23 07:07:21 |
• **facebookresearch/fastMRI** - 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 |
• **greenelab/deep-review** - learning, genomics, manubot, manuscript, neural-networks, review` 1235 271 129 HTML Unknown LICENSE.md 2018-03-12 15:06:48 |
• **shenwei356/seqkit** - platform and ultrafast toolkit for FASTA/Q file manipulationbioinformatics, cross-platform, fasta, fastq, golang, manipulation, sequence, tool, toolkit 1226 157 26 Go MIT license 2024-05-17 15:59:35 |
• **MultiQC/MultiQC** - visualization, multiqc, pypi, python, quality-control, reporting, seqera, vizualisation` 1185 582 37 JavaScript GPL-3.0 license 2024-05-31 18:30:12 |
• **dcm4che/dcm4che** - 04-22 10:59:11 |
• **scverse/scvi-tools** - cell and spatial omics datacite-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 |
• **vgteam/vg** - graph, genomics, graph, variation-graph` 1072 191 48 C++ specific 2024-05-20 18:50:28 |
• **schrodinger/pymol-open-source** - source foundation of the user-sponsored PyMOL molecular visualization system. 1071 260 C Other 2024-06-06 19:36:48 |
• **scipipe/scipipe** - efficient pipelines using Go and the commandlinebioinformatics, 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 |
• **shenwei356/csvtk** - platform, efficient and practical CSV/TSV toolkit in Golangbioinformatics, command-line, cross-platform, csv, golang, tool, toolkit, tsv 972 85 25 Go MIT license 2024-05-29 15:30:38 |
• **bigdatagenomics/adam** - data, bioinformatics, genomics, java, parquet, python, r, scala, spark` 967 304 Scala Apache License 2.0 2024-03-23 13:27:52 |
• **broadinstitute/cromwell** - description-language, workflow-execution` 965 351 112 Scala BSD-3-Clause LICENSE.txt 2024-05-07 17:47:13 |
• **hail-is/hail** - native genomic dataframes and batch computingbioinformatics, genetics, genomics, gwas, hail, python, software, vcf 946 238 55 Python MIT license 2024-06-05 17:48:05 |
• **broadinstitute/picard** - 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 |
• **aqlaboratory/proteinnet** - learning, machine-learning, protein-sequence, protein-structure, proteins` 849 130 Python MIT License 2020-11-18 23:43:32 |
• **shenwei356/rush** - platform command-line tool for executing jobs in parallelbioinformatics, command, cross-platform, execute, golang, parallel, pipeline, shell, windows 834 63 20 Go MIT license 2023-11-13 17:53:58 |
• **evo-design/evo** - 04-30 22:35:34 |
• **PaddlePaddle/PaddleHelix** - 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 |
• **samtools/htslib** - throughput sequencing data formatsbam, bcf, bioinformatics, cram, htslib, ngs, sam, vcf 779 448 C Other 2024-06-06 15:40:15 |
• **google/nucleus** - 08-31 23:19:33 |
• **nroduit/Weasis** - 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 |
• **baidu-research/NCRF** - random-fields, deep-learning, pathology, whole-slide-imaging` 749 184 37 Python Apache-2.0 license 2018-06-17 18:22:34 |
• **AstraZeneca/chemicalx** - 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 |
• **samtools/hts-specs** - throughput sequencing file formats 627 173 TeX 2024-06-06 06:50:26 |
• **samtools/bcftools** - 06-07 13:13:17 |
• **insilicomedicine/GENTRL** - 04-28 11:58:05 |
• **shenwei356/awesome** - science, git, golang, linux, perl, programing-language, python` 593 163 35 MIT license 2023-09-25 02:09:01 |
• **chanzuckerberg/cellxgene** - cell transcriptomics datadataviz, scientific, scrna-seq, transcriptomics, visualization 591 111 33 JavaScript MIT license 2023-12-19 22:19:07 |
• **invesalius/invesalius3** - 2.0 license 2022-04-14 02:28:31 |
• **lh3/bioawk** - analysis` 582 121 C 2022-08-11 01:06:45 |
• **MolecularAI/aizynthfinder** - reactions, cheminformatics, monte-carlo-tree-search, neural-networks, reaction-informatics` 548 125 Python MIT License 2024-06-03 13:34:33 |
• **owkin/PyDESeq2** - seq DEA.bioinformatics, differential-expression, python, rna-seq, transcriptomics 533 58 Python MIT License 2024-06-06 01:43:52 |
• **broadinstitute/infercnv** - Cell RNA-Seq 520 159 42 R specific 2020-02-07 20:29:28 |
• **scverse/anndata** - science, machine-learning, scanpy, scverse, transcriptomics` 511 148 Python BSD 3-Clause "New" or "Revised" License 2024-06-07 16:03:50 |
• **soedinglab/hh-suite** - 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 |
• **chhylp123/hifiasm** - resolved assembler for accurate Hifi readsbioinformatics, denovo-assembly, genomics, hifi-read, pacbio 490 84 28 C++ MIT license 2024-05-06 14:29:45 |
• **insitro/redun** - engineering, data-science, docker, etl, gcp, ml, python, workflow-engine` 489 40 Python Apache License 2.0 2024-06-06 18:52:56 |
• **biosustain/potion** - Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngineflask, flask-extensions, mongoengine, peewee, sqlalchemy 488 51 Python Other 2019-04-23 17:00:39 |
• **google-deepmind/alphamissense** - 2.0 license |
• **scverse/squidpy** - 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 |
• **lh3/minigraph** - to-graph mapper and graph generatorbioinformatics, genome-graph, genomics, pan-genome, sequence-alignment 394 38 C MIT License 2024-05-22 00:59:12 |
• **benevolentAI/guacamol** - 02-11 08:59:38 |
• **calico/basenji** - 05-28 20:08:23 |
• **ome/bioformats** - 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 |
• **MolecularAI/GraphINVENT** - 03-11 11:55:32 |
• **chembl/chembl_webresource_client** - client` 356 95 Python Other 2024-02-26 15:44:57 |
• **shenwei356/taxonkit** - style taxdump files for custom taxonomies like GTDB/ICTVbioinformatics, cross-platform, lca, lineage, taxdump, taxid, taxonkit, taxonomy 342 29 10 Go MIT license 2024-04-25 17:15:34 |
• **deepchem/DeepLearningLifeSciences** - 09-17 05:10:37 |
• **MolecularAI/Reinvent** - design, neural-networks, reinforcement-learning, transfer-learning` 332 108 Python Apache License 2.0 2023-10-19 05:26:16 |
• **aqlaboratory/rgn** - to-end differentiable learning of protein structuredeep-learning, deep-neural-networks, protein-structure, protein-structure-prediction 326 89 Python MIT License 2019-08-01 14:17:59 |
• **tencent-ailab/grover** - Supervised Graph Transformer on Large-Scale Molecular Data 313 68 7 Python specific 2021-01-18 09:06:32 |
• **lh3/miniprot** - alignment` 305 16 C MIT License 2024-04-12 21:01:25 |
• **Roche/pyreadstat** - dataframe, python, readstat, sas7bdat, spss, stata-files` 303 55 C Other 2024-06-04 09:55:07 |
• **lh3/miniasm** - assembly, genomics` 293 68 TeX MIT License 2023-12-13 01:35:58 |
• **chanzuckerberg/MedMentions**
• **AstraZeneca/rexmex** - 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 |
• **samtools/htsjdk** - 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 |
• **shenwei356/brename** - platform command-line tool for safely batch renaming files/directories via regular expressionbatch, batch-rename, batch-rename-files, batch-renamer, go, golang, rename, safe, windows 254 21 6 Go MIT license 2024-04-14 08:22:45 |
• **lh3/wgsim** - 09-03 14:58:22 |
• **Acellera/htmd** - discovery, htmd, molecular-simulations` 250 58 Rich Text Format Other 2024-06-07 15:24:26 |
• **DeepGraphLearning/GearNet** - neural-networks, pre-training, protein-representation-learning` 249 26 10 Python MIT license |
• **MolecularAI/REINVENT4** - 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 |
• **rdkit/rdkit-tutorials** - 03-19 13:36:55 |
• **insightsengineering/rtables** - 06-07 21:27:39 |
• **Bayer-Group/cloudformation-template-generator** - safe Scala DSL for generating CloudFormation templates 211 71 Scala BSD 3-Clause "New" or "Revised" License 2022-07-29 11:32:04 |
• **pharmaverse/admiral** - trials, open-source, r` 207 53 R Apache License 2.0 2024-06-07 18:23:44 |
• **OpenGene/awesome-bio-datasets** - bio-datasets 207 42 MIT License 2017-10-28 12:32:15 |
• **OpenGene/AfterQC** - trimming, bioinformatics, error, fastq, filtering, ngs, overlap, qc, quality-control, sequencing, trimming` 203 50 Python MIT License 2020-05-14 07:15:54 |
• **Bayer-Group/etcd-aws-cluster** - Clause "New" or "Revised" License 2017-02-01 01:09:05 |
• **modernatx/seqlike** - sequences, biopython, machine-learning, sequence` 202 18 Python Apache License 2.0 2024-02-16 13:13:05 |
• **scverse/scirpy** - cell TCR and BCR data. 202 31 Python BSD 3-Clause "New" or "Revised" License 2024-06-06 06:21:35 |
• **lh3/gfatools** - graph, genomics` 201 18 C 2024-02-20 15:29:14 |
• **scverse/muon** - 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 |
• **aws-samples/aws-batch-genomics** - 2.0 license 2018-11-29 18:40:42 |
• **rdkit/mmpdb** - 04-30 10:55:30 |
• **Acellera/moleculekit** - discovery, machine-learning, molecular-modeling, molecular-simulation, molecule, proteins` 193 35 Python Other 2024-06-04 13:53:30 |
• **bioinform/somaticseq** - genomics, somatic-variants` 189 53 Python BSD 2-Clause "Simplified" License 2024-05-30 07:55:34 |
• **MolecularAI/Chemformer** - 05-29 14:43:33 |
• **owkin/FLamby** - 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 |
• **ome/openmicroscopy** - 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 |
• **AstraZeneca-NGS/VarDict** - 01-05 14:06:13 |
• **scverse/spatialdata** - Clause "New" or "Revised" License 2024-06-08 00:23:48 |
• **haowenz/chromap** - profiles, genomics, sequence-analysis` 184 18 7 C++ MIT license 2024-02-06 15:29:20 |
• **chao1224/MoleculeSTM** - 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 |
• **openpharma/visR** - 06-04 13:48:59 |
• **chembl/ChEMBL_Structure_Pipeline** - 10-25 15:20:47 |
• **AstraZeneca/awesome-drug-discovery-knowledge-graphs** - list, drug-discovery, drug-discovery-knowledge-graph, knowledge-graph` 177 19 Apache License 2.0 2023-09-10 16:33:40 |
• **lh3/biofast** - 12-09 14:10:44 |
• **shenwei356/kmcp** - scale sequence/genome searchingbigsi, 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 |
• **rgcgithub/regenie** - wide association studies. 172 49 C++ Other 2024-04-03 13:52:31 |
• **soedinglab/metaeuk** - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomicsbioinformatics, eukaryotes, gene-discovery, gene-prediction, metagenomics 171 24 C GNU General Public License v3.0 2024-05-30 09:04:06 |
• **recursionpharma/gflownet** - learning, gflownet, graph-neural-network, pytorch` 168 34 Python MIT License 2024-06-06 13:29:06 |
• **scverse/scanpy-tutorials** - 06-03 19:42:01 |
• **bioinform/neusomatic** - neural-networks, deep-learning, genomics, somatic-variants` 167 50 Python Other 2021-12-23 10:41:50 |
• **lh3/readfq** - line FASTA/Q reader in several programming languagesbioinformatics, sequence-analysis 166 60 C 2021-06-06 07:27:15 |
• **insightsengineering/teal** - trials, nest, r, shiny, webapp` 164 29 R Other 2024-06-07 12:49:26 |
• **lh3/cgranges** - 05-28 21:47:37 |
• **lh3/kmer-cnt** - mer counters for tutorial purposesbioinformatics, genomics, k-mer-counting 161 13 C++ MIT License 2020-03-10 16:24:06 |
• **greenelab/tybalt** - cancer gene expression dataanalysis, 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 |
• **aqlaboratory/genie** - models, protein-design` 154 18 Python Apache License 2.0 2024-04-21 13:48:25 |
• **DeepGraphLearning/ConfGF**
• **benevolentAI/DeeplyTough** - models, deep-learning, drug-discovery, metric-learning, protein-structure` 151 39 Python Other 2023-04-07 09:33:44 |
• **chao1224/GraphMVP** - 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 |
• **OpenGene/MutScan** - 02-10 01:52:44 |
• **MolecularAI/ReinventCommunity** - design, jupyter-notebook, neural-networks, reinforcement-learning, transfer-learning` 145 57 Jupyter Notebook MIT License 2022-04-22 16:44:35 |
• **lh3/psmc** - genetics` 145 60 C Other 2022-11-21 04:39:31 |
• **tencent-ailab/DrugOOD** - aided Drug Discovery 145 19 6 Python specific |
• **ome/ome-zarr-py** - 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 |
• **Novartis/tidymodules** - Oriented approach to Shiny modulescommunication, inheritance, oop, r, shiny, shiny-modules, tidy-operators 141 11 R Other 2023-02-23 15:04:31 |
• **aws-samples/aws-genomics-workflows** - functions, workflows` 140 106 19 Shell MIT-0 license 2022-03-30 21:38:09 |
• **MolecularAI/deep-molecular-optimization** - optimization, multi-property-optimization, seq2seq, transformer` 139 36 Python Apache License 2.0 2023-03-16 07:05:06 |
• **AstraZeneca/SubTab** - 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 |
• **johnsonandjohnson/Bodiless-JS** - 01-24 03:00:32 |
• **Benson-Genomics-Lab/TRF** - 01-16 20:44:26 |
• **lh3/pangene** - 05-29 00:13:01 |
• **owkin/HistoSSLscaling** - 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 |
• **AstraZeneca/awesome-shapley-value** - 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 |
• **lh3/bedtk** - 05-28 21:48:28 |
• **Bioconductor/Contributions** - 09-12 18:32:10 |
• **Merck/BioPhi** - 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 |
• **soedinglab/plass** - assembler` 129 14 C GNU General Public License v3.0 2024-04-16 20:44:12 |
• **benevolentAI/guacamol_baselines** - 02-16 09:40:42 |
• **AstraZeneca-NGS/VarDictJava** - 01-05 14:03:51 |
• **lh3/ksw2** - alignment` 124 24 C Other 2023-06-27 17:21:12 |
• **chao1224/ChatDrug** - 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 |
• **rdkit/rdkit-js** - 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 |
• **blazerye/DrugAssist** - for-science, drug-discovery, instruction-datasets, instruction-tuning, large-language-models, molecule-generation, molecule-optimization` 123 10 3 Python |
• **bigdatagenomics/mango** - 12-02 22:21:57 |
• **OpenGene/repaq** - high compression ratio 120 20 C MIT License 2023-09-22 02:48:34 |
• **Bioconductor/BiocStickers** - feel free to contribute and/or modify.bioconductor, stickers 119 86 R Other 2024-05-10 05:58:21 |
• **greenelab/pancancer** - typesanalysis, 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 |
• **Roche/BalancedLossNLP** - 06-12 21:51:15 |
• **Merck/deepbgc** - 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 |
• **benevolentAI/MolBERT** - 06-06 10:28:35 |
• **genentech/equifold** - Grained Structure Representationmachine-learning, proteins, structural-biology, structure-prediction 116 15 Python Apache License 2.0 2023-01-08 19:51:30 |
• **OpenGene/GeneFuse** - 02-21 08:07:06 |
• **biosustain/cameo** - computer aided metabolic engineering & optimization 113 42 Python Apache License 2.0 2022-11-07 14:54:19 |
• **EBI-Metagenomics/emg-viral-pipeline** - 05-08 20:10:03 |
• **OpenGene/gencore** - sequencing, duplex, duplex-sequencing, duplication, ngs, sequencing, sequencing-error, sequencing-noise, somatic` 109 32 C++ MIT License 2023-10-27 06:19:21 |
• **OpenGene/fastv** - 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 |
• **lh3/yak** - mer analyzerbioinformatics, k-mer 108 8 C MIT License 2024-04-01 21:39:44 |
• **lh3/fermikit** - assembly, genomics, variant-calling` 108 23 TeX Other 2020-11-30 22:57:56 |
• **Merck/Halyard** - 01-23 16:59:32 |
• **ome/ngff** - 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 |
• **soedinglab/CCMpred** - 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 |
• **lh3/minimap** - 09-20 14:15:02 |
• **chao1224/Geom3D** - 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 |
• **phuse-org/phuse-scripts** - 08-01 15:21:20 |
• **chembl/FPSim2** - search` 104 17 Python MIT License 2024-02-15 11:13:05 |
• **bayer-science-for-a-better-life/Img2Mol** - 03-24 18:07:41 |
• **Biogen-Inc/tidyCDISC** - 09-22 15:18:20 |
• **openpharma/mmrm** - 06-03 18:02:15 |
• **MolecularAI/DockStream** - design, jupyter-notebook, molecular-docking, reinforcement-learning` 100 30 Python Apache License 2.0 2023-03-16 07:07:10 |
• **Bayer-Group/paquo** - QuPath and Python conversationsdigital-pathology, python, qupath 100 16 Python GNU General Public License v3.0 2024-06-02 18:21:27 |
• **genentech/gReLU** - 06-07 20:29:13 |
• **lh3/hickit** - cell Hi-C (Dip-C) and general Hi-Cbioinformatics, genomics, hi-c 98 11 C 2021-02-04 01:47:43 |
• **aqlaboratory/rgn2** - 11-28 17:16:23 |
• **lh3/bgt** - genomebioinformatics, genomics 96 10 C MIT License 2019-09-04 19:43:27 |
• **scverse/rapids_singlecell** - 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 |
• **shenwei356/bio_scripts** - 02-12 13:21:47 |
• **EBISPOT/OLS** - api` 95 40 JavaScript Apache License 2.0 2023-04-28 20:09:19 |
• **Sanofi-Public/CodonBERT** - 05-03 19:24:06 |
• **OpenGene/scrnapip** - Cell RNA Sequencing Analysis 94 14 HTML 2023-10-16 01:24:06 |
• **EBI-Metagenomics/genomes-catalogue-pipeline** - 06-06 09:44:21 |
• **samtools/tabix** - 08-03 14:29:38 |
• **shenwei356/BlackheartedHospital** - 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 |
• **AbSciBio/unlocking-de-novo-antibody-design** - 01-09 17:36:19 |
• **schrodinger/gpusimilarity** - analysis` 91 26 C++ BSD 3-Clause "New" or "Revised" License 2024-01-24 19:08:08 |
• **lh3/dipcall** - based variant calling pipeline for a pair of phased haplotype assemblies 91 9 JavaScript MIT License 2021-06-06 20:36:10 |
• **Bioconductor/CSAMA** - 06-06 12:04:08 |
• **AstraZeneca/onto_merger** - networks, biology, graph, kg, knowledge, knowledge-graph, mapping, ontology, ontology-alignment` 89 5 HTML Apache License 2.0 2024-01-11 19:22:08 |
• **hoelzer-lab/rnaflow** - Seq differential gene expression pipeline using Nextflow 89 19 HTML GNU General Public License v3.0 2024-02-26 20:45:37 |
• **shenwei356/perfect-bioinformatic-tools** - 03-19 10:22:54 |
• **Sanofi-IADC/whispr** - 06-04 12:01:03 |
• **calico/scBasset** - 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 |
• **shenwei356/bio** - performance bioinformatics package in Golangbioinformatics, golang, minimizer, package, scaled-minhash, sequence, syncmer, taxdump, taxonomy 88 9 7 Go MIT license 2024-03-11 09:41:44 |
• **owkin/HE2RNA_code** - 07-06 20:53:24 |
• **scverse/pertpy** - cell` 87 19 Python MIT License 2024-06-08 08:07:34 |