csawUsersGuide

DOI:10.18129/B9.bioc.csawUsersGuide

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, seecsawUsersGuide.

csaw User's Guide

Bioconductor version: 3.11

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

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 appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("csawUsersGuide")

PDF

R Script

User's guide

Details

biocViews	EpigeneticsWorkflow,Workflow
Version	1.4.0
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

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	csawUsersGuide_1.4.0.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	//www.andersvercelli.com/packages/csawUsersGuide/
Package Downloads Report	Download Stats