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@carmonalab Cancer Systems Immunology Lab

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    39 repositories

    • ProjecTILs

      Public
      Interpretation of cell states using reference single-cell maps
      R
      •
      GNU General Public License v3.0
      •29•253•12•0•Updated Nov 19, 2024Nov 19, 2024

    • GeneNMF

      Public
      Methods to discover gene programs on single-cell data
      R
      •3•85•7•0•Updated Nov 19, 2024Nov 19, 2024

    • Course_scRNA-seq_Exercise1

      Public
      This is the first exercise for the bioinformatics scRNA-seq course
      R
      •0•1•0•0•Updated Nov 13, 2024Nov 13, 2024

    • UCell

      Public
      Gene set scoring for single-cell data
      R
      •
      GNU General Public License v3.0
      •16•138•4•0•Updated Nov 1, 2024Nov 1, 2024

    • scooter

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

    • HiTME

      Public
      High-resolution Tumor Micro-Environment cell type classification and compositional analysis for scRNA-seq
      R
      •0•4•1•0•Updated Oct 18, 2024Oct 18, 2024

    • HiTME_CaseStudies

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

    • scGate_models

      Public
      Cell type gating models for scGate
      scgate
      3•3•3•0•Updated Sep 30, 2024Sep 30, 2024

    • ProjecTILs_CaseStudies

      Public
      A repository of case studies using ProjecTILs
      R
      •3•13•0•0•Updated Jul 26, 2024Jul 26, 2024

    • GeneNMF.demo

      Public
      Demos and applications for NMF on single-cell data
      CSS
      •0•0•0•0•Updated Jul 19, 2024Jul 19, 2024

    • DC_atlas

      Public
      Python
      •1•0•0•0•Updated Jul 5, 2024Jul 5, 2024

    • .github

      Public
      0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

    • scGate

      Public
      marker-based purification of cell types from single-cell RNA-seq datasets
      signaturesfilteringmarker-genesscgatesingle-cell
      R
      •12•93•2•0•Updated Jun 9, 2024Jun 9, 2024

    • Yerly_BCC_wounding

      Public
      Code to reproduce the results by Yerly et al. (2024)
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 3, 2024Jun 3, 2024

    • SignatuR

      Public
      A database of useful gene signatures for single-cell analysis
      R
      •0•20•2•0•Updated Mar 28, 2024Mar 28, 2024

    • ProjecTILs.demo

      Public
      A repository for testing the functionalities of ProjecTILs
      CSS
      •0•0•1•0•Updated Mar 27, 2024Mar 27, 2024

    • UCell_demo

      Public
      R
      •1•1•1•0•Updated Mar 1, 2024Mar 1, 2024

    • TILPRED

      Public
      Tumor-Infiltrating CD8 Lymphocytes states prediction
      R
      •
      GNU General Public License v3.0
      •3•12•0•0•Updated Feb 7, 2024Feb 7, 2024

    • STACAS.demo

      Public
      Integrating scRNA-seq data using STACAS
      R
      •0•0•0•0•Updated Feb 2, 2024Feb 2, 2024

    • STACAS

      Public
      R package for semi-supervised single-cell data integration
      R
      •
      GNU General Public License v3.0
      •9•76•3•0•Updated Feb 2, 2024Feb 2, 2024

    • scGate.demo

      Public
      CSS
      •2•4•0•0•Updated Jan 19, 2024Jan 19, 2024

    • CD8_human_TIL_atlas_construction

      Public
      Python
      •0•3•0•0•Updated Dec 19, 2023Dec 19, 2023

    • scib-pipeline

      Public
      Snakemake pipeline that works with the scIB package to benchmark data integration methods.
      Jupyter Notebook
      •
      MIT License
      •28•0•0•0•Updated Dec 18, 2023Dec 18, 2023

    • scIntegrationMetrics

      Public
      R implementation of integration metrics for single-cell data
      R
      •
      GNU General Public License v3.0
      •5•3•0•0•Updated Dec 18, 2023Dec 18, 2023

    • LiTang_IL10_CART

      Public
      0•2•0•0•Updated Oct 10, 2023Oct 10, 2023

    • seurat-wrappers

      Public
      Community-provided extensions to Seurat
      R
      •
      GNU General Public License v3.0
      •131•0•0•0•Updated Apr 27, 2023Apr 27, 2023

    • Tcell_clonal_analysis

      Public
      Reproducible code for reference-based T cell clonal analysis
      GNU General Public License v3.0
      •0•2•0•0•Updated Apr 12, 2023Apr 12, 2023

    • human_CD8_TIL_CaseStudies

      Public
      Projection example using a human CD8 TIL reference map.
      referenceprojectils
      R
      •0•2•0•0•Updated Mar 3, 2023Mar 3, 2023

    • GEEP_Jesus_Nov2021

      Public
      R
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • scib-pipeline-2

      Public
      Snakemake pipeline that works with the scIB package to benchmark data integration methods.
      Python
      •
      MIT License
      •28•0•0•0•Updated Feb 23, 2023Feb 23, 2023