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Achievement: Pull SharkAchievement: Starstruckx2

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@carmonalab

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mass-a/README.md

Hi I'm Massimo 👋

I'm a computational biologist @ Carmona lab at the Ludwig Institute for Cancer Research, Department of Oncology of the University of Lausanne, and at the Swiss Institute of Bioinformatics. Currently my work is focused on the development of tools for single-cell biology and on their application to improve our understanding of immune responses in cancer and infection.

Here are some of the tools I developed (or contributed to):

Single-cell biology

  • GeneNMF: unsupervised discovery of gene programs by non-negative matrix factorization. GitHub - CRAN - Preprint
  • UCell: robust and scalable single-cell gene signature scoring. GitHub - Bioconductor - Paper
  • scGate: marker-based purification or classification of cell populations in single-cell data. GitHub - CRAN - Paper
  • STACAS: semi-supervised integration (batch-effect correction) of single-cell transcriptomics data. GitHub - Paper1 - Paper2
  • ProjecTILs: reference-based analysis of single-cell transcriptomics data. GitHub - Paper
  • SPICA: web portal to explore our immune cell reference maps and to project into them your own data Website - Paper
  • SignatuR: a database of useful gene signatures for single-cell analysis. GitHub

T-cell epitope prediction

  • NetMHC: binding of peptides to MHC class I molecules. Webserver - Paper
  • NetMHCpan: pan-specific prediction of peptide-MHC class I binding. Webserver - Paper
  • NetMHCIIpan: pan-specific prediction of peptide-MHC class II binding. Webserver - Paper
  • NetH2pan: prediction of peptide interactions with murine MHC class I (H2) molecules. Webserver - Paper
  • MHC II automated benchmarks: automated benchmarking of MHC class II prediction tools @ IEDB. Webpage - Paper

Immunopeptidomics

  • GibbsCluster: simultaneous alignment and clustering of peptide data. Webserver - Paper1 - Paper2
  • NNAlign: identifying sequence motifs in quantitative peptide data. Webserver - Paper
  • MS-rescue: computational pipeline to increase the quality and yield of immunopeptidomics experiments Download - Paper

Massimo's GitHub stats Top Langs

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  1. carmonalab/UCell carmonalab/UCell Public

    Gene set scoring for single-cell data

    R 141 16

  2. carmonalab/ProjecTILs carmonalab/ProjecTILs Public

    Interpretation of cell states using reference single-cell maps

    R 255 30

  3. carmonalab/scGate carmonalab/scGate Public

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

    R 97 13

  4. carmonalab/STACAS carmonalab/STACAS Public

    R package for semi-supervised single-cell data integration

    R 77 9

  5. scRepertoire scRepertoire Public

    Forked from ncborcherding/scRepertoire

    A toolkit for single-cell immune profiling

    R

  6. carmonalab/GeneNMF carmonalab/GeneNMF Public

    Methods to discover gene programs on single-cell data

    R 89 4