bioc-issue-bot
commented
1 month ago Hi @HDash
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: MotifPeeker
Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Version: 0.99.0
Authors@R: c(
person(given = "Hiranyamaya",
family = "Dash",
role = c("cre", "aut"),
email = "hdash.work@gmail.com",
comment = c(ORCID = "0009-0005-5514-505X")),
person(given = "Thomas",
family = "Roberts",
role = c("aut"),
email = "tomroberts.work15@gmail.com",
comment = c(ORCID = "0009-0006-6244-8670")),
person(given = "Nathan",
family = "Skene",
role = c("aut"),
email = "nathan.skene@gmail.com",
comment = c(ORCID = "0000-0002-6807-3180"))
)
Description: MotifPeeker is used to compare and analyse datasets from
epigenomic profiling methods with motif enrichment as the key
benchmark. The package outputs an HTML report consisting of three
sections: (1. General Metrics) Overview of peaks-related general
metrics for the datasets (FRiP scores, peak widths and motif-summit
distances). (2. Known Motif Enrichment Analysis) Statistics for the
frequency of user-provided motifs enriched in the datasets. (3.
De-Novo Motif Enrichment Analysis) Statistics for the frequency of
de-novo discovered motifs enriched in the datasets and compared with
known motifs.
License: GPL (>= 3)
URL: https://github.com/neurogenomics/MotifPeeker
BugReports: https://github.com/neurogenomics/MotifPeeker/issues
Depends:
R (>= 4.4.0)
Imports:
BiocFileCache,
BiocParallel,
DT,
ggplot2,
plotly,
universalmotif,
GenomicRanges,
IRanges,
rtracklayer,
tools,
htmltools,
rmarkdown,
viridis,
SummarizedExperiment,
htmlwidgets,
Rsamtools,
GenomicAlignments,
GenomeInfoDb,
Biostrings,
BSgenome,
memes,
S4Vectors,
magrittr,
dplyr,
purrr,
tidyr,
heatmaply,
stats,
utils
Suggests:
BiocStyle,
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38,
downloadthis,
knitr,
markdown,
methods,
remotes,
rworkflows,
testthat (>= 3.0.0),
withr,
emoji,
curl,
jsonlite
VignetteBuilder:
knitr
biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
MultipleComparison, FunctionalGenomics, MotifDiscovery,
SequenceMatching, Software, Alignment
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: FALSE
RoxygenNote: 7.3.2
SystemRequirements: MEME Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html>
lshep
HDash
jwokaty
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