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@carmonalab

Cancer Systems Immunology Lab

At Ludwig Cancer Research Lausanne and Department of Oncology, University of Lausanne & Swiss Institute of Bioinformatics

Cancer Systems Immunology laboratory

We study patterns of variation across cancer patients to identify general principles of the immune system regulation during tumor progression. We combine innovative data science with high-throughput single-cell and spatial omics technologies to reveal biological insight and develop predictive models of disease progression and response to treatment.

We are part of the Ludwig Institute for Cancer Research, Department of Oncology of the University of Lausanne, and the Swiss Institute of Bioinformatics. Our lab is located at the new Agora Cancer Research Center in beautiful Lausanne, Switzerland.

Overview of our lab's tools:

  • GeneNMF: unsupervised discovery of gene programs in omics data by non-negative matrix factorization (NMF). It can be especially useful to extract recurrent gene programs in cancer cells, which are otherwise difficult to integrate and analyse jointly.

  • SignatuR: a database of useful gene signatures for single-cell analysis. It also provides utilities to store and interact with gene signatures.

  • UCell: robust and scalable single-cell gene signature scoring, uses positive and negative genes and mitigates data sparsity by nearest neighbors smoothing. For easy retrieval and storing of signatures we recommend SignatuR.

  • scGate: the tool for marker-based purification or classification of cell populations. Use pre-defined gating models or create your own to purify a cell type or to classify into multiple cell types.

  • STACAS: accurate integration (batch-effect correction) of single-cell transcriptomics data. Its semi-supervised mode takes advantage of prior cell type knowledge to guide integration. To assess quality of integration, scIntegrationMetrics provides multiple useful metrics.

  • ProjecTILs: reference-based analysis framework, 1) select or build your reference map, 2) project new data into the map without altering it. Then 3) obtain high-resolution subtype classifications, 4) explore how cell states in projected data deviate from the reference, and optionally, 5) upgrade your reference to include novel cell states.

  • SPICA: web portal to explore our immune cell reference maps and to project into them your own data

Pinned Loading

  1. STACAS STACAS Public

    R package for semi-supervised single-cell data integration

    R 75 9

  2. ProjecTILs ProjecTILs Public

    Interpretation of cell states using reference single-cell maps

    R 250 29

  3. UCell UCell Public

    Gene set scoring for single-cell data

    R 137 16

  4. scGate scGate Public

    marker-based purification of cell types from single-cell RNA-seq datasets

    R 92 12

  5. HiTME HiTME Public

    High-resolution Tumor Micro-Environment cell type classification and compositional analysis for scRNA-seq

    R 4

  6. GeneNMF GeneNMF Public

    Methods to discover gene programs on single-cell data

    R 81 3

Repositories

Showing 10 of 39 repositories
  • Course_scRNA-seq_Exercise1 Public

    This is the first exercise for the bioinformatics scRNA-seq course

    carmonalab/Course_scRNA-seq_Exercise1’s past year of commit activity
    R 1 0 0 0 Updated Nov 12, 2024
  • GeneNMF Public

    Methods to discover gene programs on single-cell data

    carmonalab/GeneNMF’s past year of commit activity
    R 81 3 6 0 Updated Nov 11, 2024
  • UCell Public

    Gene set scoring for single-cell data

    carmonalab/UCell’s past year of commit activity
    R 137 GPL-3.0 16 3 0 Updated Nov 1, 2024
  • scooter Public
    carmonalab/scooter’s past year of commit activity
    R 2 GPL-3.0 0 7 0 Updated Oct 30, 2024
  • HiTME Public

    High-resolution Tumor Micro-Environment cell type classification and compositional analysis for scRNA-seq

    carmonalab/HiTME’s past year of commit activity
    R 4 0 0 0 Updated Oct 18, 2024
  • HiTME_CaseStudies Public

    Repository of case studies using HiTME

    carmonalab/HiTME_CaseStudies’s past year of commit activity
    CSS 0 0 0 0 Updated Sep 30, 2024
  • scGate_models Public

    Cell type gating models for scGate

    carmonalab/scGate_models’s past year of commit activity
    3 3 3 0 Updated Sep 30, 2024
  • ProjecTILs Public

    Interpretation of cell states using reference single-cell maps

    carmonalab/ProjecTILs’s past year of commit activity
    R 250 GPL-3.0 29 13 0 Updated Sep 16, 2024
  • ProjecTILs_CaseStudies Public

    A repository of case studies using ProjecTILs

    carmonalab/ProjecTILs_CaseStudies’s past year of commit activity
    R 13 3 0 0 Updated Jul 26, 2024
  • GeneNMF.demo Public

    Demos and applications for NMF on single-cell data

    carmonalab/GeneNMF.demo’s past year of commit activity
    CSS 0 0 0 0 Updated Jul 19, 2024

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