CAGEr

DOI:10.18129/B9.bioc.CAGEr

This is thedevelopmentversion of CAGEr; for the stable release version, seeCAGEr.

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Bioconductor version: Development (3.16)

Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

Author: Vanja Haberle [aut], Charles Plessy [cre], Damir Baranasic [ctb], Sarvesh Nikumbh [ctb]

Maintainer: Charles Plessy

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("CAGEr")

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("CAGEr")

HTML	R Script	CAGEr: an R package for CAGE data analysis and promoterome mining
HTML	R Script	Use of CAGE resources with CAGEr
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering,FunctionalGenomics,GeneExpression,Normalization,Preprocessing,Sequencing,Software,Transcription,Visualization
Version	2.3.0
In Bioconductor since	BioC 2.12 (R-3.0) (9 years)
License	GPL-3
Depends	methods,MultiAssayExperiment, R (>= 4.1.0)
Imports	BiocGenerics,BiocParallel,BSgenome,data.table,DelayedArray,DelayedMatrixStats,formula.tools,GenomeInfoDb,GenomicAlignments,GenomicRanges(>= 1.37.16),ggplot2(>= 2.2.0),gtools,IRanges(>= 2.18.0),KernSmooth,memoise,plyr,Rsamtools,reshape2,rtracklayer,S4Vectors(>= 0.27.5),som,stringdist,stringi,SummarizedExperiment, utils,vegan,VGAM
LinkingTo
Suggests	BSgenome.Drerio.UCSC.danRer7,DESeq2,FANTOM3and4CAGE,BiocStyle,knitr,rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	seqPattern
Links To Me
Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	CAGEr_2.3.0.tar.gz
Windows Binary	CAGEr_2.3.0.zip
macOS 10.13 (High Sierra)	CAGEr_2.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CAGEr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CAGEr
Package Short Url	//www.anjoumacpherson.com/packages/CAGEr/
Package Downloads Report	Download Stats