DOI: 10.18129/B9.bioc.CAGEr    

This is the development version of CAGEr; for the stable 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: Development (3.7)

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

Author: Vanja Haberle <vanja.haberle at>

Maintainer: Vanja Haberle <vanja.haberle at>, Charles Plessy <plessy at>

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biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 1.21.5
In Bioconductor since BioC 2.12 (R-3.0) (5 years)
License GPL-3
Depends methods, R (>= 2.15.0)
Imports beanplot, BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, GenomicRanges(>= 1.23.16), ggplot2 (>= 2.2.0), gtools, IRanges(>= 2.5.27), KernSmooth, memoise, MultiAssayExperiment, plyr, Rsamtools, reshape, rtracklayer, S4Vectors, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM
Suggests BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me seqPattern
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