CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Bioconductor version: Release (3.20)
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
Author: Vanja Haberle [aut], Charles Plessy [cre], Damir Baranasic [ctb], Sarvesh Nikumbh [ctb]
Maintainer: Charles Plessy <charles.plessy at oist.jp>
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization |
| Version | 2.12.0 |
| 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, Biostrings, BSgenome, CAGEfightR, data.table, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges(>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges(>= 2.18.0), KernSmooth, memoise, plyr, rlang, Rsamtools, reshape2, rtracklayer, S4Vectors(>= 0.27.5), scales, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | seqPattern |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CAGEr_2.12.0.tar.gz |
| Windows Binary (x86_64) | CAGEr_2.12.0.zip |
| macOS Binary (x86_64) | CAGEr_2.12.0.tgz |
| macOS Binary (arm64) | CAGEr_2.11.5.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/ |
| Package Downloads Report | Download Stats |