ChromSCape
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ChromSCape.
Analysis of single-cell epigenomics datasets with a Shiny App
Bioconductor version: 3.16
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("ChromSCape")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("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")| ChromSCape | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Annotation, BatchEffect, ChIPSeq, Classification, Clustering, DifferentialPeakCalling, Epigenetics, GeneSetEnrichment, MethylSeq, MultipleComparison, Normalization, Pathways, Preprocessing, PrincipalComponent, QualityControl, ReportWriting, ShinyApps, SingleCell, Software, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray |
| System Requirements | |
| URL | https://github.com/vallotlab/ChromSCape |
| Bug Reports | https://github.com/vallotlab/ChromSCape/issues |
See More
| Suggests | testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChromSCape_1.8.0.tar.gz |
| Windows Binary | ChromSCape_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | ChromSCape_1.8.0.tgz |
| macOS Binary (arm64) | ChromSCape_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChromSCape |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChromSCape |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChromSCape/ |
| Package Short Url | https://bioconductor.org/packages/ChromSCape/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |