Closed PFPrzytycki closed 2 years ago
Hi @PFPrzytycki
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: CellWalkR
Type: Package
Date: 2022-11-1
Title: An R Package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
Version: 0.99.0
Authors@R: person(given="Pawel F.", family="Przytycki", role=c("aut","cre"), email="pawel.przytycki@gladstone.ucsf.edu")
Description: CellWalkR is an R package that integrates single-cell open chromatin (scATAC-seq) data with cell type labels and bulk epigenetic data to identify cell type-specific regulatory regions. A GPU implementation and downsampling strategies enable thousands of cells to be processed in seconds. CellWalkR’s user-friendly interface provides interactive analysis and visualization of cell labels and regulatory region mappings.
License: GPL-2 + file LICENSE
Encoding: UTF-8
Depends:
R (>= 4.0.0),
GenomicRanges (>= 1.40.0)
Imports:
data.table,
Matrix,
Suggests:
SnapATAC,
ArchR,
cicero,
Seurat (>= 3.0),
tensorflow,
ggplot2,
scales,
reshape2,
Rtsne,
uwot,
igraph,
dendextend,
circlize,
plotly,
shiny,
parallel,
knitr,
rmarkdown
RoxygenNote: 7.1.2
VignetteBuilder: knitr
LazyData: true
biocViews: SingleCell, ATACSeq, Software
SnapATAC and ArchR are not in CRAN or Bioconductor. Do you know if they will be distributed in one of those systems? We cannot allow dependencies to github-only packages.
As far as I am aware, those packages will not be available on CRAN or Bioconductor in the immediate future. These packages are only required for a set of data loading functions. Is there an acceptable way to not include the packages in the DESCRIPTION file but require a user to install them if they use those particular functions?
Sorry, we don't allow this. All software required by Bioconductor packages must be present at a regulated repository; currently these are limited to CRAN and Bioconductor. You may want to speak to the developers of those packages to see about their plans. If you find another way to accomplish the data loading without those packages please reopen this issue with detailed reply to this comment. Thank you
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