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    12 repositories

    • AP1_Multi_Chemopersistence_TNBC

      Public
      AP-1 drives a recurrent drug persister state in triple negative breast cancer
      HTML
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • BRCA1_Tumorigenesis

      Public
      scripts to reproduce analysis from Landragin et al
      R
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • scCUT-Tag_10X

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • 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
      •0•3•0•0•Updated Jul 2, 2024Jul 2, 2024

    • scNanoCUTTag_10X

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jun 21, 2024Jun 21, 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
      •
      Other
      •1•4•0•0•Updated May 14, 2024May 14, 2024

    • ChromSCape

      Public
      ChromSCape
      single-cellepigenomicsshiny
      R
      •8•14•2•1•Updated Jan 22, 2024Jan 22, 2024

    • benchmark_scepigenomics

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•9•0•0•Updated Mar 14, 2023Mar 14, 2023

    • bulk_Epigenomics

      Public
      Snakemake pipelines to process FASTQ files from bulk epigenomicsd
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 13, 2022Dec 13, 2022

    • ChemoPersistance

      Public
      Scripts to analyze single-cell and bulk RNA & ChIP-seq of TNBC under drug treatment
      R
      •2•6•0•0•Updated Feb 8, 2022Feb 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
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 15, 2020Sep 15, 2020

    • scChIPseq

      Public
      Analysis of single-cell ChIP-seq datasets : From count matrices to differential analysis
      R
      •5•20•1•0•Updated Jun 2, 2020Jun 2, 2020