celldex

[LTLA]

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

• Repository: https://github.com/LTLA/celldex

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 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.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @LTLA

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: celldex
Title: Reference Index for Cell Types 
Version: 0.99.0
Date: 2020-05-24
Authors@R: c(person("Dvir", "Aran", email="dvir.aran@ucsf.edu", role=c("aut")),
    person("Aaron", "Lun", email="infinite.monkeys.with.keyboards@gmail.com", role=c("aut", "cre", "cph")),
    person("Daniel", "Bunis", role="aut"),
    person("Jared", "Andrews", email = "jared.andrews07@gmail.com", role="aut"),
    person("Friederike", "Dündar", email = "frd2007@med.cornell.edu", role="aut"))
Description: 
    Provides a collection of reference expression datasets with curated cell
    type labels, for use in procedures like automated annotation of single-cell
    data or deconvolution of bulk RNA-seq.
License: GPL-3 
Depends: SummarizedExperiment
Imports: 
    utils,
    ExperimentHub,
    AnnotationHub,
    AnnotationDbi,
    S4Vectors,
    DelayedArray,
    DelayedMatrixStats
Suggests:
    testthat,
    knitr,
    rmarkdown,
    BiocStyle,
    DT
biocViews: 
    ExperimentHub,
    ExperimentData, 
    ExpressionData, 
    SequencingData, 
    RNASeqData
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://github.com/LTLA/celldex
BugReports: https://support.bioconductor.org/
RoxygenNote: 7.1.0

[LTLA]

To give some context, this contains getters for ExperimentHub datasets that were originally distributed via SingleR. I've moved them into another package for more general use by other Bioconductor packages and to cut the dependency tree for SingleR itself.

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/LTLA.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("celldex"). The package 'landing page' will be created at

https://bioconductor.org/packages/celldex

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.