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 (3.15)

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>, Charles Plessy <charles.plessy at>, Damir Baranasic <damir.baranasic at>, Sarvesh Nikumbh <s.nikumbh at>

Maintainer: Charles Plessy <charles.plessy at>

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


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biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 2.1.0
In Bioconductor since BioC 2.12 (R-3.0) (8.5 years)
License GPL-3
Depends methods, MultiAssayExperiment, R (>= 4.1.0)
Imports BiocGenerics, BiocParallel, BSgenome, 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
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