1.deepchem / deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
- drug-discovery
- quantum-chemistry
- deep-learning
- biology
- materials-science
- hacktoberfest
+228 stars
from 6,895 · score 5.43
Trending repositories
Ranked by Attention Score: stars gained over the last 90 complete days
42 repositories by Attention Score · Aug 7, 2026 – Nov 4, 2026 (UTC)
2.jwohlwend / boltz
Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
+159 stars
from 4,133 · score 5.08
+86 stars
from 1,813 · score 4.47
+56 stars
from 1,606 · score 4.04
+55 stars
from 2,227 · score 4.03
6.mims-harvard / PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
- dataset
- graph-machine-learning
- +2 more
+37 stars
from 801 · score 3.64
7.songlab-cal / gpn
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
+37 stars
from 350 · score 3.64
8.RosettaCommons / RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
+35 stars
from 2,247 · score 3.58
9.snap-stanford / GEARS
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
+33 stars
from 389 · score 3.53
10.snap-stanford / UCE
UCE is a zero-shot foundation model for single-cell gene expression data
+29 stars
from 322 · score 3.40
11.OATML-Markslab / ProteinGym
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
- protein-fitness
+28 stars
from 456 · score 3.37
12.Teichlab / celltypist
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
- cell-type-classification
- label-transfer
+17 stars
from 500 · score 2.89
13.facebookresearch / esmArchived
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
+16 stars
from 4,160 · score 2.83
14.hail-is / hail
Cloud-native genomic dataframes and batch computing
- genetics
- vcf
- genomics
- gwas
- bioinformatics
- python
- +2 more
+14 stars
from 1,068 · score 2.71
15.KangBoming / BulkFormer
BulkFormer: A large-scale foundation model for human bulk transcriptomes
+14 stars
from 73 · score 2.71
16.microsoft / evodiff
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
+13 stars
from 676 · score 2.64
17.gao-lab / GLUE
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
+13 stars
from 473 · score 2.64
18.Martinsos / edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
- c-plus-plus
- alignment-path
- +2 more
+10 stars
from 602 · score 2.40
+10 stars
from 425 · score 2.40
+10 stars
from 142 · score 2.40
21.agemagician / ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
+9 stars
from 1,314 · score 2.30
22.ElliotXie / CASSIA
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
- retrieved-augmented-generation
- singlecell
- +7 more
+9 stars
from 100 · score 2.30
23.shmlkv / dna-claude-analysis
Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.
- analysis
- claude
- claudecode
- dna
- genome
+9 stars
from 51 · score 2.30
24.vcflib / vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
- haplotypecaller
+8 stars
from 681 · score 2.20
25.shenwei356 / taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
- lca
- taxid
- +2 more
+8 stars
from 476 · score 2.20
26.kreshuklab / panseg
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
- bioimage-analysis
- image-segmentation
- +1 more
+8 stars
from 129 · score 2.20
27.snap-stanford / SATURN
The repository host gives no description.
+7 stars
from 169 · score 2.08
28.theislab / chemCPA
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
- disentanglement
- drug-discovery
- genomics
- perturbation
- single-cell
- transfer-learning
+7 stars
from 155 · score 2.08
29.peizhenbai / DrugBAN
Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
+6 stars
from 147 · score 1.95
30.bebop / poly
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
- bioengineering
- computational-biology
- +14 more
+5 stars
from 731 · score 1.79
31.labomics / midas
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
- deep-generative-model
- deep-learning
- single-cell-data-integration
- single-cell-multiomics
+4 stars
from 71 · score 1.61
32.cafferychen777 / ChatSpatial
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
- python
- single-cell
- +14 more
+4 stars
from 41 · score 1.61
33.OpenBioLink / OpenBioLink
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
+3 stars
from 161 · score 1.39
34.bowang-lab / scGPT-spatial
The repository host gives no description.
+3 stars
from 141 · score 1.39
35.RucDongLab / STAGATE
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
+3 stars
from 52 · score 1.39
36.myzhengSIMM / TranSiGen
The repository host gives no description.
+3 stars
from 36 · score 1.39
37.bcbio / bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
+2 stars
from 1,028 · score 1.10
38.ebi-webcomponents / nightingale
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
- biohackeu22
+2 stars
from 150 · score 1.10
39.angelolab / ark-analysis
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
+2 stars
from 108 · score 1.10
40.SuperBianC / scMulan
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
+2 stars
from 62 · score 1.10
+2 stars
from 58 · score 1.10
42.BoevaLab / CancerFoundation
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
- cancer
- foundation-model
- single-cell
+2 stars
from 30 · score 1.10