bioc-issue-bot
commented
2 years ago Hi @snikumbh
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Type: Package
Package: seqArchRplus
Title: Downstream analyses of promoter sequence architectures and HTML
report generation
Version: 0.99.0
Authors@R:
person("Sarvesh", "Nikumbh", , "sarvesh.nikumbh@gmail.com",
role = c("aut", "cre", "cph"),
comment = c(ORCID = "0000-0003-3163-4447"))
Description: seqArchRplus enables downstream analyses of promoter
sequence architectures/clusters identified by seqArchR (or any other
tool/method). With additional available information such as the TPM values
and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus
can order the input promoter clusters by their shape (IQWs), and write the
cluster information as browser/IGV track files. Provided visualizations
are of two kind: per sample/stage and per cluster visualizations. Those of
the first kind include: plot panels for each sample showing per cluster
shape, TPM and other score distributions, sequence logos, and peak
annotations. The second include per cluster chromosome-wise and strand
distributions, motif occurrence heatmaps and GO term enrichments.
Additionally, seqArchRplus can also generate HTML reports for easy viewing
and comparison of promoter architectures between samples/stages (future).
License: GPL-3 | file LICENSE
URL: https://snikumbh.github.io/seqArchRplus/,
https://github.com/snikumbh/seqArchRplus
BugReports: https://github.com/snikumbh/seqArchRplus/issues
Depends:
R (>= 4.2.1),
GenomicRanges,
IRanges,
S4Vectors
Imports:
BiocParallel,
Biostrings,
BSgenome,
ChIPseeker,
cli,
clusterProfiler,
cowplot,
factoextra,
forcats,
GenomeInfoDb,
ggplot2,
graphics,
grDevices,
gridExtra,
heatmaps,
methods,
RColorBrewer,
scales,
seqArchR,
seqPattern,
stats,
utils
Suggests:
BSgenome.Dmelanogaster.UCSC.dm6,
BiocStyle,
CAGEr (>= 2.0.2),
covr,
knitr (>= 1.22),
org.Dm.eg.db,
pdftools,
rmarkdown (>= 1.12),
slickR,
svglite,
testthat (>= 3.0.2),
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
vdiffr (>= 0.3.0),
xfun
VignetteBuilder:
knitr
biocViews: Annotation, Visualization, ReportWriting, GO, MotifAnnotation,
Clustering
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.2
vjcitn
snikumbh
lshep
jwokaty
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