bioc-issue-bot
commented
6 months ago Hi @brianSroberts
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:
Package: DegCre
Type: Package
Title: Probabilistic association of DEGs to CREs from differential data
Version: 0.99.0
Date: 2023-12-04
Authors@R: person(given="Brian S.",
family="Roberts",
email = "brianroberts1976@yahoo.com",
role = c("aut", "cre"),
comment=c(ORCID = "0009-0001-2914-6826"))
Maintainer@R: person(given="Brian S.",
family="Roberts",
email = "brianroberts1976@yahoo.com",
comment=c(ORCID = "0009-0001-2914-6826"))
Description:
DegCre generates associations between differentially expressed genes (DEGs)
and cis-regulatory elements (CREs) based on non-parametric concordance
between differential data. The user provides GRanges of DEG TSS and CRE
regions with differential p-value and optionally log-fold changes and
DegCre returns an annotated Hits object with associations and their
calculated probabilities. Additionally, the package provides functionality
for visualization and conversion to other formats.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.3
Depends: R (>= 4.2.1)
URL: https://github.com/brianSroberts/DegCre
Imports:
GenomicRanges,
InteractionSet,
plotgardener,
S4Vectors,
stats,
graphics,
grDevices
biocViews:
GeneExpression,
GeneRegulation,
ATACSeq,
ChIPSeq,
DNaseSeq,
RNASeq
Suggests:
BSgenome,
BSgenome.Hsapiens.UCSC.hg38,
org.Hs.eg.db,
knitr,
rmarkdown,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
lshep
brianSroberts
jianhong
jwokaty
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[ x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[ x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[ x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[ x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[ x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[ x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[ x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.