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csawUsersGuide

This is the development version of csawUsersGuide; for the stable release version, see csawUsersGuide.

csaw User's Guide


Bioconductor version: Development (3.19)

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 (from within R, enter citation("csawUsersGuide")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script

Details

biocViews EpigeneticsWorkflow, Workflow
Version 1.19.0
License GPL-3
Depends
Imports
System Requirements
URL
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Suggests knitr, BiocStyle, BiocManager
Linking To
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Package Archives

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

Source Package csawUsersGuide_1.19.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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