ChromSCape
This is the released version of ChromSCape; for the devel version, see ChromSCape.
Analysis of single-cell epigenomics datasets with a Shiny App
Bioconductor version: Release (3.23)
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.pr at gmail.com>
citation("ChromSCape")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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
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_1.22.0.tar.gz |
| Windows Binary (x86_64) | ChromSCape_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | ChromSCape_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | ChromSCape_1.22.0.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 |