DEScan2
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see DEScan2.
Differential Enrichment Scan 2
Bioconductor version: 3.11
Integrated peak and differential caller, specifically designed for broad epigenomic signals.
Author: Dario Righelli [aut, cre], John Koberstein [aut], Bruce Gomes [aut], Nancy Zhang [aut], Claudia Angelini [aut], Lucia Peixoto [aut], Davide Risso [aut]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
citation("DEScan2")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DEScan2")
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("DEScan2")| DEScan2 Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, Epigenetics, ImmunoOncology, PeakDetection, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), GenomicRanges |
| Imports | BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors(>= 0.23.19), SummarizedExperiment, tools, utils |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod |
| Linking To | Rcpp, RcppArmadillo |
| 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 | DEScan2_1.8.0.tar.gz |
| Windows Binary | DEScan2_1.8.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | DEScan2_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DEScan2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DEScan2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/DEScan2/ |
| Package Short Url | https://bioconductor.org/packages/DEScan2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |