scider

[ningbioinfo]

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

• Repository: https://github.com/ChenLaboratory/scider

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[bioc-issue-bot]

Hi @ningbioinfo

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: scider
Type: Package
Title: Spatial cell-type inter-correlation by density in R
Version: 0.99.0
Authors@R: 
    c(person(given = "Ning", 
  family = "Liu",
  role = c("aut"),
  email = "liu.n@wehi.edu.au",
  comment = c(ORCID = "0000-0002-9487-9305")),
      person(given = "Mengbo",
   family = "Li",
   role = c("aut"),
   email = "li.me@wehi.edu.au",
   comment = c(ORCID = "0000-0002-9666-5810")),
      person(given = "Yunshun",
   family = "Chen",
   role = c("aut", "cre"),
   email = "yuchen@wehi.edu.au",
   comment = c(ORCID = "0000-0003-4911-5653")))
Description: scider is an user-friendly R package providing functions 
    to model the global density of cells in a slide of spatial 
    transcriptomics data. All functions in the package are built 
    based on the SpatialExperiment object, allowing integration into 
    various spatial transcriptomics-related packages from Bioconductor. 
    After modelling density, the package allows for serveral 
    downstream analysis, including colocalization analysis, 
    boundary detection analysis and differential density analysis.
biocViews: Spatial, Transcriptomics
License: GPL-3 + file LICENSE
URL: https://github.com/ChenLaboratory/scider, https://chenlaboratory.github.io/scider/
BugReports: https://github.com/ChenLaboratory/scider/issues
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports:
    SpatialExperiment,
    SummarizedExperiment,
    spatstat.geom,
    spatstat.explore,
    sf,
    lwgeom, 
    ggplot2,
    stats,
    pheatmap,
    plotly,
    shiny,
    igraph,
    janitor,
    knitr,
    methods,
    utils,
    rlang,
    isoband,
    S4Vectors,
    grDevices
Suggests:
    edgeR,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Depends: 
    R (>= 4.3)
VignetteBuilder: knitr

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): scider_0.99.0.tar.gz macOS 12.6.5 Monterey: scider_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/scider to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[lshep]

Minor comment. We would recommend. Its highly recommended to have a more unique title for the vignette rather than Quick_start to avoid potential naming conflicts with other packages. We generally suggest the same name as the package.
This however does not prevent the package from being accepted for the release; please consider changing at your earliest convenience.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[lshep]

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/ningbioinfo.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("scider"). The package 'landing page' will be created at

https://bioconductor.org/packages/scider

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.