csawUsersGuide

DOI: 10.18129/B9.bioc.csawUsersGuide    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see csawUsersGuide.

csaw User's Guide

Bioconductor version: 3.12

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>

Installation

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

if (!requireNamespace("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")

 

PDF

R Script

User's guide

Details

biocViews	EpigeneticsWorkflow, Workflow
Version	1.6.0
License	GPL-3
Depends
Imports
LinkingTo
Suggests	csaw, chipseqDBData, edgeR, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, rtracklayer, Rsamtools, Gviz, knitr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	csawUsersGuide_1.6.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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