1.scverse / scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
- single-cell-genomics
- single-cell-rna-seq
- +4 more
+53 stars
from 1,667 · score 3.99
Trending repositories
Ranked by Attention Score: stars gained over the last 90 complete days
16 repositories by Attention Score · Aug 7, 2026 – Nov 4, 2026 (UTC)
2.kexinhuang12345 / DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
- covid19
- virtual-screening
- +13 more
+30 stars
from 1,171 · score 3.43
3.scverse / squidpy
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
- image-analysis
- data-visualization
- +2 more
+25 stars
from 587 · score 3.26
4.CSOgroup / cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
+19 stars
from 185 · score 3.00
5.fish-quant / big-fish
Toolbox for the analysis of smFISH images.
- pattern-classification
- rna-localization
- segmentation
- smfish
- spatial-features
- spot-detection
+13 stars
from 78 · score 2.64
6.kexinhuang12345 / MolTrans
MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
+12 stars
from 239 · score 2.56
7.theislab / scvelo
RNA Velocity generalized through dynamical modeling
+10 stars
from 504 · score 2.40
8.theislab / nicheformer
Repository for Nicheformer: a foundation model for single-cell and spatial omics
+10 stars
from 169 · score 2.40
9.weigertlab / spotiflow
Accurate and efficient spot detection for microscopy data
+10 stars
from 138 · score 2.40
10.theislab / scarches
Reference mapping for single-cell genomics
- single-cell
- deep-learning
- rna-seq-analysis
- data-integration
- batch-correction
- multimodal-deep-learning
- +4 more
+9 stars
from 405 · score 2.30
11.broadinstitute / cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
- workflow-execution
- workflow
- cloud
- hpc
- bioinformatics
- executor
- +7 more
+7 stars
from 1,076 · score 2.08
12.songlab-cal / tape
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
- benchmark
- language-modeling
- +2 more
+5 stars
from 741 · score 1.79
+5 stars
from 703 · score 1.79
14.cytomining / pycytominer
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
- cellprofiler
- image-analysis
- +1 more
+2 stars
from 144 · score 1.10
15.theislab / ncem
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
- encoder-decoder-model
- scanpy
- +3 more
+1 stars
from 120 · score 0.69
16.theislab / multigrate
Multigrate: multiomic data integration for single-cell genomics
+1 stars
from 34 · score 0.69