csawUsersGuide
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see csawUsersGuide.
csaw User's Guide
Bioconductor version: 3.10
A user's guide for the csaw package for detecting differentially bound regions in ChIP-seq data. Describes how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("csawUsersGuide")
):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("csawUsersGuide")
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("csawUsersGuide")
User's guide | R Script |
Details
biocViews | EpigeneticsWorkflow, Workflow |
Version | 1.2.0 |
License | GPL-3 |
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Imports | |
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URL |
See More
Suggests | csaw, chipseqDBData, edgeR, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, rtracklayer, Rsamtools, Gviz, knitr, BiocStyle |
Linking To | |
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Depends On Me | |
Imports Me | |
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Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | csawUsersGuide_1.2.0.tar.gz |
Windows Binary | |
Mac OS X 10.11 (El Capitan) | |
Source Repository | git clone https://git.bioconductor.org/packages/csawUsersGuide |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/csawUsersGuide |
Package Short Url | https://bioconductor.org/packages/csawUsersGuide/ |
Package Downloads Report | Download Stats |