ChromSCape

DOI: 10.18129/B9.bioc.ChromSCape    

Analysis of single-cell epigenomics datasets with a Shiny App

Bioconductor version: Release (3.12)

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Author: Pacome Prompsy [aut, cre] , Celine Vallot [aut]

Maintainer: Pacome Prompsy <pacome.prompsy at curie.fr>

Citation (from within R, enter citation("ChromSCape")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChromSCape")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChromSCape")

 

HTML R Script ChromSCape
PDF   Reference Manual
Text   NEWS

Details

biocViews ATACSeq, Annotation, BatchEffect, ChIPSeq, Classification, Clustering, DifferentialPeakCalling, Epigenetics, GeneSetEnrichment, MethylSeq, MultipleComparison, Normalization, Pathways, Preprocessing, PrincipalComponent, QualityControl, ReportWriting, SingleCell, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, qualV, stringdist, fs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr
LinkingTo
Suggests testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL https://github.com/vallotlab/ChromSCape
BugReports https://github.com/vallotlab/ChromSCape/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ChromSCape_1.0.0.tar.gz
Windows Binary ChromSCape_1.0.0.zip
macOS 10.13 (High Sierra) ChromSCape_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChromSCape
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChromSCape
Package Short Url https://bioconductor.org/packages/ChromSCape/
Package Downloads Report Download Stats

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