DOI: 10.18129/B9.bioc.CAGEr  

This package is for version 3.17 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: 3.17

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>

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HTML R Script CAGEr: an R package for CAGE data analysis and promoterome mining
HTML R Script Use of CAGE resources with CAGEr
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biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 2.6.1
In Bioconductor since BioC 2.12 (R-3.0) (10.5 years)
License GPL-3
Depends methods, MultiAssayExperiment, R (>= 4.1.0)
Imports BiocGenerics, BiocParallel, BSgenome, CAGEfightR, data.table, DelayedArray, DelayedMatrixStats,, 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
Suggests BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me seqArchRplus, seqPattern
Links To Me
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