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recoup : An R package for the creation of complex genomic profile plots

Package: recoup
Type: Package
Title: An R package for the creation of complex genomic profile plots
Author: Panagiotis Moulos <moulos@fleming.gr>
Maintainer: Panagiotis Moulos <moulos@fleming.gr>
Depends: GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap
Imports: BiocGenerics, biomaRt, circlize, rtracklayer, plyr
Suggests: grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown,
zoo, RUnit, BiocInstaller, BSgenome, RSQLite, RMySQL
Enhances: parallel
Description: recoup calculates and plots signal profiles
created from short sequence reads derived from Next
Generation Sequencing technologies. The profiles
provided are either sumarized curve profiles or heatmap
profiles. Currently, recoup supports genomic profile
plots for reads derived from ChIP-Seq and RNA-Seq
experiments. The package uses ggplot2 and ComplexHeatmap
graphics facilities for curve and heatmap coverage
profiles respectively.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
URL: https://github.com/pmoulos/recoup
biocViews: Software, GeneExpression, Preprocessing, QualityControl,
RNASeq, ChIPSeq, Sequencing, Coverage
VignetteBuilder: knitr
Authors@R: c(person(given="Panagiotis", family="Moulos",
email="moulos@fleming.gr", role=c("aut", "cre")))
Version: 1.0.2
Date: 2016-04-02
Collate: 'annotation.R' 'argcheck.R' 'coverage.R' 'ranges.R' 'recoup.R'
'plot.R' 'profile.R' 'util.R'
NeedsCompilation: no
Packaged: 2016-05-16 06:04:00 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: ChIPSeq, Coverage, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
● 0 images, 17 functions, 1 datasets
● Reverse Depends: 0

EnrichedHeatmap : Making Enriched Heatmaps

Package: EnrichedHeatmap
Type: Package
Title: Making Enriched Heatmaps
Version: 1.2.2
Date: 2016-4-27
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Depends: R (>= 3.1.2), grid, ComplexHeatmap (>= 1.9.7), GenomicRanges,
IRanges, locfit
Imports: methods, matrixStats, stats, GetoptLong
Suggests: testthat (>= 0.3), knitr, markdown, circlize (>= 0.3.1)
VignetteBuilder: knitr
Description: Enriched heatmap is a special type of heatmap which
visualizes the enrichment of genomic signals on specific target regions.
Here we implement enriched heatmap by ComplexHeatmap package.
Since this type of heatmap is just a normal heatmap but with some special settings,
with the functionality of ComplexHeatmap, it would be much easier
to customize the heatmap as well as concatenating to a list of heatmaps to
show correspondance between different data sources.
biocViews: Software, Visualization, Sequencing, GenomeAnnotation,
Coverage
URL: https://github.com/jokergoo/EnrichedHeatmap
License: GPL (>= 2)
Packaged: 2016-05-16 05:44:36 UTC; biocbuild
Repository: Bioconductor
Date/Publication: 2016-4-27 00:00:00
NeedsCompilation: no

● Data Source: BioConductor
● BiocViews: Coverage, GenomeAnnotation, Sequencing, Software, Visualization
● 3 images, 20 functions, 0 datasets
● Reverse Depends: 0