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vallotlab

Popular repositories

  1. scChIPseq scChIPseq Public

    Analysis of single-cell ChIP-seq datasets : From count matrices to differential analysis

    R 20 5

  2. ChromSCape ChromSCape Public

    ChromSCape

    R 14 8

  3. benchmark_scepigenomics benchmark_scepigenomics Public

    Jupyter Notebook 8

  4. ChemoPersistance ChemoPersistance Public

    Scripts to analyze single-cell and bulk RNA & ChIP-seq of TNBC under drug treatment

    R 6 2

  5. scChIPseq_DataEngineering scChIPseq_DataEngineering Public

    This pipeline is dedicated to create single-cell count matrix from paired-end raw fastQ files coming from single-cell ChIP-seq experiments.

    Shell 4 1

  6. IDclust IDclust Public

    IDclust is an unsupervised method for clustering single-cell datasets (scRNA, scEpigenome). The cells are iteratively re-processed and re-clustered. Subclusters are created provided they are signif…

    R 2

Repositories

Showing 9 of 9 repositories
  • ChromSCape Public

    ChromSCape

    R 14 8 2 1 Updated Jan 22, 2024
  • scChIPseq_DataEngineering Public

    This pipeline is dedicated to create single-cell count matrix from paired-end raw fastQ files coming from single-cell ChIP-seq experiments.

    Shell 4 1 0 0 Updated Jan 12, 2024
  • BRCA1_Tumorigenesis Public

    scripts to reproduce analysis from Landragin et al

    R 0 0 0 0 Updated Nov 17, 2023
  • benchmark_scepigenomics Public
    Jupyter Notebook 8 Apache-2.0 0 0 0 Updated Mar 14, 2023
  • IDclust Public

    IDclust is an unsupervised method for clustering single-cell datasets (scRNA, scEpigenome). The cells are iteratively re-processed and re-clustered. Subclusters are created provided they are significantly different from each other.

    R 2 0 0 0 Updated Feb 13, 2023
  • bulk_Epigenomics Public

    Snakemake pipelines to process FASTQ files from bulk epigenomicsd

    Python 0 GPL-3.0 0 0 0 Updated Dec 13, 2022
  • ChemoPersistance Public

    Scripts to analyze single-cell and bulk RNA & ChIP-seq of TNBC under drug treatment

    R 6 2 0 0 Updated Feb 8, 2022
  • ChromSCape_benchmarking Public

    Scripts and dataset to reproduce benchmarking of SnapATAC, CisTopic, Cusanovich2018 and EpiScanpy & scOrange on single-cell H3K27me3 cell mix from 'Interactive analysis of single-cell epigenomic landscapes with ChromSCape'

    R 0 GPL-3.0 1 0 0 Updated Sep 15, 2020
  • scChIPseq Public

    Analysis of single-cell ChIP-seq datasets : From count matrices to differential analysis

    R 20 5 1 0 Updated Jun 2, 2020

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