1.scverse / squidpySpatial Single Cell Analysis in Pythonsingle-cell-rna-seqsingle-cell-genomicsspatial-transcriptomicsspatial-analysisimage-analysisdata-visualization+2 morePythonBSD-3-CLAUSE613 total128 forks+50 starsfrom 563 · score 3.93
2.Dana-Farber-AIOS / pathmlTools for computational pathologymachine-learningdigital-pathologycomputational-pathologybiomedical-image-processingpathologyhistopathology+9 morePythonGPL-2.0467 total87 forks+16 starsfrom 451 · score 2.83
3.kharchenkolab / numbatHaplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiomecancer-genomicscnv-detectionsingle-cellphylogenysingle-cell-analysissingle-cell-rna-seq+4 moreROther license233 total37 forks+16 starsfrom 217 · score 2.83
4.cafferychen777 / ChatSpatialMCP server for spatial transcriptomics analysis through natural language interfaces.bioinformaticscell-communicationdeconvolutionmachine-learningpythonsingle-cell+14 morePythonMIT45 total14 forks+13 starsfrom 32 · score 2.64
5.cafferychen777 / flashdeconvFast, deterministic cell-type deconvolution for million-bin spatial transcriptomicsbioinformaticscell-type-deconvolutioncomputational-biologydeconvolutionpythonscanpy+3 morePythonBSD-3-CLAUSE26 total0 forks+9 starsfrom 17 · score 2.30