CAGEr specifications

Information


Unique identifier OMICS_07118
Name CAGEr
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.22.3
Stability Stable
Requirements
methods, plyr, BiocGenerics, Rsamtools, utils, R(>=2.15.0), S4Vectors, GenomeInfoDb, rtracklayer, BiocStyle, GenomicAlignments, SummarizedExperiment, BiocParallel, DESeq2, BSgenome, gtools, data.table, rmarkdown, knitr, KernSmooth, beanplot, reshape, DelayedArray, BSgenome.Drerio.UCSC.danRer7, VGAM, som, IRanges(>=2.5.27), GenomicRanges(>=1.23.16), vegan, ggplot2(>=2.2.0), memoise, MultiAssayExperiment, stringdist, stringi, FANTOM3and4CAGE
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Vanja Haberle <>

Publication for CAGEr

CAGEr in publications

 (7)
PMCID: 5951944
PMID: 29760402
DOI: 10.1038/s41598-018-25748-3

[…] san diego, ca, usa). cage tags were mapped to the mouse genome (mm10) using bowtie2 version 2.2.5. ctsss, which corresponded to promoter candidates, were identified using the bioconductor package, cager, version 1.14.0 and bsgenome.mmusculus.ucsc.mm10, version 1.4.0. cage tag counts per ctss were plotted as scatter plots and pearson correlations between all possible pairs of samples […]

PMCID: 5483264
PMID: 28646867
DOI: 10.1186/s12864-017-3863-7

[…] leading:3 trailing:3 slidingwindow:4:10 leading:3 trailing:3 minlen:20. then, the trimmed reads were mapped to the usmarcv1.0 reference genome using star (v2.4.1a) []. the r/bioconductor package cager (v1.14.0) [] was used to obtain transcription starting site (tss) clusters, as described in its documentation. sequences of 50 bases that flanked the dominant tss of each tss cluster […]

PMCID: 5499205
PMID: 28561034
DOI: 10.1038/ncomms15656

[…] to the human genome build hg19/grch37 tophat (v1.4.1). bru-seq data from induced samples were compared with uninduced samples and fold differences determined., cage data were analysed with the cager package. briefly, after bam file preprocessing and quality (mappingq≥20) filtering, cage tags were normalized and tsss distance-based clustering (20 bp distance) was performed. then, aggregate […]

PMCID: 5201198
PMID: 27869827
DOI: 10.1038/ng.3719

[…] h3k9ac, in the epigenome roadmap dataset. specifically, the fantom dataset heart samples were cnhs11758, cnhs11757, cnhs10621, cnhs10653, cnhs12855, cnhs12856 and cnhs12857 and were downloaded using cager. these were then processed using cager (standard parameters) in order to identify tsss by first normalising the tag counts using a power law and then clustering the reads in order to find cage […]

PMCID: 4978467
PMID: 27504829
DOI: 10.1371/journal.pgen.1006231

[…] compiled from the ucsc mm9 refseq annotation [,]. then, cage clusters were computed based on the "fantom3and4"/"fantomtimecoursecagemouse"/"liver_under_constant_darkness" data set as provided by the cager/fantom3and4cage r packages [], using the recommended procedures in the package. cage peak widths were computed for locations ±300 bp of the tsss provided by the ucsc refseq annotation, using […]


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CAGEr institution(s)
Department of Biology, University of Bergen, Bergen, Norway; Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London; MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London, UK; RIKEN Center for Life Science Technologies, Division of Genomic Technologies (CLST DGT), RIKEN Yokohama Campus, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Wako-shi, Saitama, Japan; Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London, UK; Department of Informatics, University of Bergen, Høyteknologisenteret, Bergen, Norway

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