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Package: ggcoverage | ||
Type: Package | ||
Package: ggcoverage | ||
Title: Visualize Genome/Protein Coverage with Various Annotations | ||
Version: 1.3.0 | ||
Authors@R: c( | ||
person(given = "Yabing", | ||
family = "Song", | ||
role = c("aut", "cre"), | ||
email = "[email protected]"), | ||
person(given = "Michael", | ||
family = "Jahn", | ||
email = "[email protected]", | ||
role = "aut", | ||
person("Yabing", "Song", , "[email protected]", role = c("aut", "cre", "cph")), | ||
person("Michael", "Jahn", , "[email protected]", role = c("aut", "cph"), | ||
comment = c(ORCID = "0000-0002-3913-153X")) | ||
) | ||
Maintainer: Yabing Song <[email protected]> | ||
Description: The goal of 'ggcoverage' is to simplify the process of visualizing genome/protein coverage. It contains functions to | ||
load data from BAM, BigWig, BedGraph or txt/xlsx files, create genome/protein coverage plot, add various annotations to | ||
the coverage plot, including base and amino acid annotation, GC annotation, gene annotation, transcript annotation, ideogram annotation, | ||
peak annotation, contact map annotation, link annotation and peotein feature annotation. | ||
Description: The goal of 'ggcoverage' is to simplify the process of | ||
visualizing genome/protein coverage. It contains functions to load | ||
data from BAM, BigWig, BedGraph or txt/xlsx files, create | ||
genome/protein coverage plots, add various annotations to the coverage | ||
plot, including base and amino acid annotation, GC annotation, gene | ||
annotation, transcript annotation, ideogram annotation, peak | ||
annotation, contact map annotation, link annotation and protein | ||
feature annotation. | ||
License: MIT + file LICENSE | ||
Encoding: UTF-8 | ||
RoxygenNote: 7.3.1 | ||
URL: https://showteeth.github.io/ggcoverage/, https://github.com/showteeth/ggcoverage | ||
URL: https://showteeth.github.io/ggcoverage/, | ||
https://github.com/showteeth/ggcoverage | ||
BugReports: https://github.com/showteeth/ggcoverage/issues | ||
biocViews: | ||
Imports: | ||
BiocParallel, | ||
Biostrings, | ||
BSgenome, | ||
dplyr, | ||
GenomeInfoDb, | ||
GenomicAlignments, | ||
GenomicRanges, | ||
ggbio, | ||
ggforce, | ||
ggh4x, | ||
ggpattern, | ||
ggplot2, | ||
ggrepel, | ||
grDevices, | ||
gridExtra, | ||
HiCBricks, | ||
IRanges, | ||
magrittr, | ||
methods, | ||
openxlsx, | ||
patchwork, | ||
RColorBrewer, | ||
reshape2, | ||
rlang, | ||
Rsamtools, | ||
rtracklayer, | ||
scales, | ||
stats, | ||
utils, | ||
methods, | ||
GenomeInfoDb, | ||
S4Vectors, | ||
Biostrings, | ||
BSgenome, | ||
GenomicAlignments, | ||
reshape2, | ||
scales, | ||
seqinr, | ||
ggforce, | ||
HiCBricks, | ||
ggpattern, | ||
BiocParallel, | ||
openxlsx, | ||
stats, | ||
stringr, | ||
gridExtra | ||
utils | ||
Suggests: | ||
rmarkdown, | ||
knitr, | ||
BiocStyle, | ||
htmltools, | ||
BSgenome.Hsapiens.UCSC.hg19, | ||
graphics, | ||
HiCDataHumanIMR90 | ||
VignetteBuilder: knitr | ||
HiCDataHumanIMR90, | ||
htmltools, | ||
knitr, | ||
rmarkdown | ||
VignetteBuilder: | ||
knitr | ||
biocViews: | ||
Encoding: UTF-8 | ||
RoxygenNote: 7.3.1 |