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Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Bioconductor version: 2.13

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

Author: Vanja Haberle, Department of Biology, University of Bergen, Norway <vanja.haberle at>

Maintainer: Vanja Haberle <vanja.haberle at>

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biocViews Clustering, HighThroughputSequencing, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 1.4.1
In Bioconductor since BioC 2.12 (R-3.0)
License GPL-3
Depends methods, R (>= 2.15.0), BSgenome, BSgenome.Mmusculus.UCSC.mm9
Imports Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM
Suggests BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, FANTOM3and4CAGE
System Requirements
Depends On Me
Imports Me
Suggests Me

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