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    49 repositories

    • pyucell

      Public
      Robust and scalable single-cell signature scoring
      pythonsignaturessingle-cellgene-modules
      Python
      •
      MIT License
      •2•13•0•0•Updated Jan 30, 2026Jan 30, 2026

    • scECODA

      Public
      Exploratory compositional data analysis of single-cell data
      R
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Jan 30, 2026Jan 30, 2026

    • scECODA_demo

      Public
      Tutorials for the scECODA package
      R
      •0•1•0•0•Updated Jan 29, 2026Jan 29, 2026

    • scTypeEval

      Public
      scTypeEval is an R package designed for the assessment and validation of cell type classifications in single-cell transcriptomics. In the absence of ground trut…
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 29, 2026Jan 29, 2026

    • STACAS.demo

      Public
      Integrating scRNA-seq data using STACAS
      R
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • STACAS

      Public
      R package for semi-supervised single-cell data integration
      R
      •
      GNU General Public License v3.0
      •9•95•4•0•Updated Jan 27, 2026Jan 27, 2026

    • carmonalab.r-universe.dev

      Public
      R-universe for carmonalab
      0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

    • pyucell_test

      Public
      Code for evaluating pyUCell
      Jupyter Notebook
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • HiTME

      Public
      High-resolution Tumor Micro-Environment cell type classification and compositional analysis for scRNA-seq
      R
      •0•6•1•0•Updated Jan 19, 2026Jan 19, 2026

    • UCell_demo

      Public
      R
      •1•1•1•0•Updated Jan 9, 2026Jan 9, 2026

    • ProjecTILs

      Public
      Interpretation of cell states using reference single-cell maps
      R
      •
      GNU General Public License v3.0
      •32•309•6•0•Updated Dec 19, 2025Dec 19, 2025

    • ProjecTILs.demo

      Public
      A repository for testing the functionalities of ProjecTILs
      CSS
      •0•0•1•0•Updated Dec 18, 2025Dec 18, 2025

    • GeneNMF.demo

      Public
      Demos and applications for NMF on single-cell data
      CSS
      •0•1•0•0•Updated Dec 2, 2025Dec 2, 2025

    • Proteasome_APlab

      Public
      A repo for bioinformatics analyses of proteasomal gene expression in TILs
      0•0•0•0•Updated Nov 27, 2025Nov 27, 2025

    • UCell

      Public
      Gene set scoring for single-cell data
      R
      •
      GNU General Public License v3.0
      •20•180•4•0•Updated Oct 31, 2025Oct 31, 2025

    • task_batch_integration

      Public
      Inclusion of ciLISI metric and STACAS method in batch integration benchmarking
      Python
      •
      MIT License
      •16•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • GeneNMF

      Public
      Methods to discover gene programs on single-cell data
      R
      •8•173•5•0•Updated Sep 26, 2025Sep 26, 2025

    • .github

      Public
      0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

    • scGate_models

      Public
      Cell type gating models for scGate
      scgate
      3•4•2•0•Updated Sep 18, 2025Sep 18, 2025

    • Gcnt2_Gut

      Public
      R
      •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • scGate

      Public
      marker-based purification of cell types from single-cell RNA-seq datasets
      signaturesfilteringsingle-cellmarker-genesscgate
      R
      •15•138•5•0•Updated Jul 23, 2025Jul 23, 2025

    • task_label_projection

      Public
      Automated cell type annotation from rich, labeled reference data
      Python
      •
      MIT License
      •4•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • SignatuR

      Public
      A database of useful gene signatures for single-cell analysis
      R
      •0•28•1•0•Updated May 19, 2025May 19, 2025

    • scIntegrationMetrics

      Public
      R implementation of integration metrics for single-cell data
      R
      •
      GNU General Public License v3.0
      •0•9•2•0•Updated Apr 15, 2025Apr 15, 2025

    • Yerly_BCC_wounding

      Public
      Code to reproduce the results by Yerly et al. (2024)
      0•5•0•0•Updated Dec 17, 2024Dec 17, 2024

    • Course_scRNA-seq_Exercise1

      Public
      This is the first exercise for the bioinformatics scRNA-seq course
      R
      •0•2•0•0•Updated Nov 13, 2024Nov 13, 2024

    • scooter

      Public
      R
      •
      GNU General Public License v3.0
      •0•2•7•0•Updated Oct 30, 2024Oct 30, 2024

    • HiTME_CaseStudies

      Public
      Repository of case studies using HiTME
      CSS
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • ProjecTILs_CaseStudies

      Public
      A repository of case studies using ProjecTILs
      R
      •3•15•0•0•Updated Jul 26, 2024Jul 26, 2024

    • DC_atlas

      Public
      Python
      •0•0•0•0•Updated Jul 5, 2024Jul 5, 2024