bioc-issue-bot
commented
1 month ago Hi @Egors01
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: DuplexDiscovereR
Title: Analysis of the data from RNA duplex probing experiments
Authors@R:
c(person("Egor", "Semenchenko", ,
email = "yegor.smb@gmail.com",
role = c("aut", "cre","cph"),
comment = c(ORCID = "0009-0007-5306-076X")),
person("Volodymyr", "Tsybulskyi", ,
email = "Volodymyr.Tsybulskyi@mdc-berlin.de", role = c("ctb"),
comment = c(ORCID = "0009-0002-4141-6291")),
person("Irmtraud M.", "Meyer", ,
email = "irmtraud.m.meyer@cantab.net", role = c("aut","cph"),
comment = c(ORCID = "0000-0002-4048-3479")))
Description:
DuplexDiscovereR is a package designed for analyzing data from RNA
cross-linking and proximity ligation protocols such as SPLASH, PARIS,
LIGR-seq, and others.
DuplexDiscovereR accepts input in the form of chimerically or
split-aligned reads. It includes procedures for alignment classification,
filtering, and efficient clustering of individual chimeric reads into duplex
groups (DGs). Once DGs are identified, the package predicts RNA duplex
formation and their hybridization energies. Additional metrics, such as
p-values for random ligation hypothesis or mean DG alignment scores,
can be calculated to rank final set of RNA duplexes.
Data from multiple experiments or replicates can be processed separately
and further compared to check the reproducibility of the experimental method.
License: GPL-3
URL: https://github.com/Egors01/Duplex_Explorer
BugReports: https://github.com/Egors01/Duplex_Explorer
Encoding: UTF-8
NeedsCompilation: no
Version: 0.99.0
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
BiocType: Software
biocViews:
Sequencing,
Transcriptomics,
StructuralPrediction,
Clustering,
SplicedAlignment
Imports:
Gviz,
Biostrings,
rtracklayer,
digest,
GenomicAlignments,
dplyr,
ggsci,
igraph,
rlang,
scales,
stringr,
tibble,
tidyr,
purrr,
methods
Depends:
R (>= 4.4),
InteractionSet
LazyData: false
Suggests:
knitr,
UpSetR,
BiocStyle,
rmarkdown,
testthat (>= 3.0.0)
VignetteBuilder: knitr
VignetteEngine: knitr
Config/testthat/edition: 3
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.