bioc-issue-bot
commented
7 months ago Hi @lodimk2
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: chai
Title: CHAI: consensus Clustering tHrough similArIty matrIx integratIon for single cell type identification
Version: 0.99.0
Authors@R:
c(person("Musaddiq", "Lodi", email = "lodimk2@vcu.edu", role = c("aut", "cre")), person("Kezie", "Osei", email = "oseika@vcu.edu", role = c("aut")), person("Vaishnavi", "Ranganathan", email = "vrangana@andrew.cmu.edu", role = c("aut")))
Description: We present CHAI (consensus Clustering tHrough similArIty matrix integratIon for single cell type identification), a wisdom of crowds approach for scRNAseq clustering. CHAI presents two methods which aggregate the clustering results from seven state of the art clustering methods: CHAI-AvgSim and CHAI-SNF. Both methods demonstrate improved performance on a diverse selection of benchmarking datasets, including outperforming a previous consensus clustering method.
License: MIT
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1.9000
Imports:
Seurat,
SeuratObject,
SingleCellExperiment,
Spectrum,
SNFtool,
aricode,
cluster,
kernlab,
mclust,
CHOIR,
RaceID,
SC3,
scSHC,
Biobase,
FNN
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
biocViews: GeneExpression, SingleCell, Clustering
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends:
R (>= 2.10)
LazyData: false
lshep
lodimk2
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.