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CITEViz-ExperimentHub #2839

Closed gartician closed 2 years ago

gartician commented 2 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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bioc-issue-bot commented 2 years ago

Hi @gartician

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: CITEVizTestData
Title: Peripheral blood CITE-Seq dataset with 10K cells for use with CITEViz tutorial
Version: 0.99.0
Date: 2022-10-11
Authors@R: c(
    person('Garth', 'Kong', email = 'kongga2017@gmail.com', role = c('cre', 'aut'), comment = c(ORCID = '0000-0001-5262-5406')),
    person('Thai', 'Nguyen', email = 'tnguye14@uoregon.edu', role = 'aut', comment = c(ORCID = '0000-0002-8988-4003')),
    person('Wesley', 'Rosales', email = 'wesleykrosales@gmail.com', role = 'aut', comment = c(ORCID = '0000-0002-6381-9844')),
    person('Anjali', 'Panikar', email = 'anjali.panikar@gmail.com ', role = 'aut', comment = c(ORCID = '0000-0002-5740-807X')),
    person('John', 'Cheney', email = 'John.h.cheney@gmail.com', role = 'aut', comment = c(ORCID = '0000-0001-6194-2745')),
    person('Sarah', 'Carratt', email = 'carratt@ohsu.edu', role = 'rev', comment = c(ORCID = '0000-0003-2493-6789')),
    person('Brittany', 'Curtiss', email = 'curtisbr@ohsu.edu', role = 'rev', comment = c(ORCID = '0000-0002-5274-8323')),
    person('Theodore', 'Braun', email = 'braunt@ohsu.edu', role = 'rev', comment = c(ORCID = '0000-0002-6248-2143')),
    person('Julia', 'Maxson', email = 'maxsonj@ohsu.edu', role = 'rev', comment = c(ORCID = '0000-0002-3871-7221'))
    )
Description: This ExperimentHub dataset is used for the CITEViz tutorial. This dataset contains peripheral blood CITE-Seq dataset with 10K cells from Hao et. al. 2021.
License: MIT + file LICENSE
Imports:
  AnnotationHub,
  ExperimentHub
RoxygenNote: 7.2.1
Suggests:
  knitr,
  BiocStyle,
  rmarkdown,
  Seurat
Language: en-US
VignetteBuilder: knitr
biocViews: SingleCell, ShinyApps, FlowCytometry, QualityControl, ExperimentHubSoftware
gartician commented 2 years ago

Hi BioConductor Admins,

Based on the suggestions in #2738, I am here to submit an ExperimentHub (EH) package as a test dataset for CITEViz. This package contains a PBMC CITE-Seq dataset with 2500 cells in either Seurat or SingleCellExperiment format. I have uploaded the datasets in RDS format to the Azure Data Lakes under CITEVizTestData. I was able to validate the EH package with ExperimentHubData::makeExperimentHubMetadata("."), devtools::build() and devtools::check(). If I am reading the documentation correctly, the man/ and vignettes/ contents are yet to be finalized right?

Thank you for looking into this.

lshep commented 2 years ago

Please submit under #2738 so the packages can be reviewed together. This is greatly expedite the process; else you would have to wait for this package to be reviewed, accepted, ingested, and on the daily builder before the associated package could find the package and continue in the review. please see Submit related packages . You would comment the line

AdditionalPackage: https://github.com/[maxsonBraunLab/CITEVizTestData](https://github.com/maxsonBraunLab/CITEVizTestData)

on the other issue.