Closed ncrna closed 2 years ago
Hi @ncrna
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: Yeskit
Type: Package
Title: Yet Another Single-Cell Analysis Toolkit (Yeskit)
Version: 0.99.0
Date: 2021-09-25
Authors@R: person(given = "Wei", family = "Zhang", role = c("cre", "aut"), email = "admin@ncrna.net")
Description: This is a single-cell analysis tookit. It can be used for
single-cell gene expression matrices importation, data integration,
clustering, differential analysis, functional analysis, and
visualization. It obeys the default data structure of Seurat, and
stores pathogen expression data and pathway enrichment scores in
the obj@meta.data slot and stores differential gene analysis results
and GO enrichment results in the obj@misc slot. Besides, Yeskit has
the option to rasterize the geom_point layer of ggplot2, while keep
all axes, labels, and text in vector format.
Depends:
R (>= 3.6.0)
Imports:
utils,
stats,
grDevices,
Seurat (>= 3.0.0),
ggplot2 (>= 3.3.0),
cowplot (>= 1.0.0),
RColorBrewer (>= 1.1.2),
dplyr (>= 0.8.5),
harmony (>= 0.1.0),
topGO (>= 2.38.1),
org.Hs.eg.db (>= 3.10.0),
org.Mm.eg.db (>= 3.10.0),
methods (>= 3.6.0),
patchwork (>= 1.0.0),
ggrepel (>= 0.8.2),
Matrix (>= 1.2.18),
MASS (>= 7.3.51.5),
scales (>= 1.1.0),
gtable (>= 0.3.0),
ggrastr (>= 0.2.3),
msigdbr (>= 7.4.1),
RANN (>= 2.6.1)
Suggests:
testthat (>= 3.0.0),
knitr,
rmarkdown
biocViews: SingleCell, Clustering, GeneExpression, DifferentialExpression, GO, Annotation, Visualization, Software
VignetteBuilder: knitr
LazyData: true
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.1
BugReports: https://github.com/ncrna/Yeskit/issues
git_url: https://github.com/ncrna/Yeskit
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Hi @ncrna,
You write in the DESCRIPTION
that Yeskit "obeys the default data structure of Seurat".
However Seurat is not a Bioconductor package and the preferred/supported data structure for single-cell data in Bioconductor is the SingleCellExperiment class.
For Yeskit to be included in Bioconductor, I think it would need to support the SingleCellExperiment class in addition to the Seurat data structure.
I think this needs to be resolved before we begin a review of the package for its suitability in Bioconductor.
Cheers, Pete
Hi @ncrna ,
I agree with @PeteHaitch . Are you planning to follow up on this submission @ncrna ?
Thanks, H.
Hi @ncrna ,
I agree with @PeteHaitch . Are you planning to follow up on this submission @ncrna ?
Thanks, H.
Dear @ncrna ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
@PeteHaitch Thank you for your suggests! We are trying to change the code to obey the SingleCellExperiment data structure.
@hpages Thank you for your suggestion! Can we fix the code follow your suggestion and resubmit next time?
You don't need to resubmit. Make sure to push your changes to git.bioconductor.org in addition to GitHub, and to bump the package version to trigger builds. Thanks
@ncrna may we expect updates soon? We like to see progress and response to reviews within a 3-4 week time frame?
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
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