CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Bioconductor version: Release (3.19)
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 | ||
| NEWS | Text |
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 |
See More
| 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/ |
| Package Downloads Report | Download Stats |