CAGEr

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CAGEr.

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

Bioconductor version: 3.19

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 <charles.plessy at oist.jp>

Citation (from within R, enter citation("CAGEr")):

Installation

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


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

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("CAGEr")

CAGEr: an R package for CAGE data analysis and promoterome mining HTML R Script

Use of CAGE resources with CAGEr HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization

Version 2.10.0

In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)

License GPL-3

Depends methods, MultiAssayExperiment, R (>= 4.1.0)

Imports BiocGenerics, BiocParallel, BSgenome, CAGEfightR, 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

System Requirements

URL

Suggests BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me seqArchRplus, seqPattern

Links To Me

Build Report Build Report

Package Archives

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

Source Package CAGEr_2.10.0.tar.gz

Windows Binary (x86_64) CAGEr_2.10.0.zip

macOS Binary (x86_64) CAGEr_2.10.0.tgz

macOS Binary (arm64) CAGEr_2.10.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/CAGEr

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CAGEr

Bioc Package Browser https://code.bioconductor.org/browse/CAGEr/

Package Short Url https://bioconductor.org/packages/CAGEr/

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