dominoSignal

[jmitchell81]

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

• Repository: https://github.com/FertigLab/dominoSignal

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[bioc-issue-bot]

Hi @jmitchell81

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: dominoSignal
Title: Cell Communication Analysis for Single Cell RNA Sequencing
Version: 0.99.2
Authors@R: c(
    person("Christopher", "Cherry", role = c("aut"), email = "ccherry.6574@gmail.com", comment = c(ORCID = "0000-0002-5481-0055")),
    person("Jacob T", "Mitchell", role = c("aut", "cre"), email = "jmitch81@jhmi.edu", comment = c(ORCID = "0000-0002-5370-9692")),
    person("Sushma", "Nagaraj", role = c("aut"), email = "snagara5@jhmi.edu", comment = c(ORCID = "0000-0001-5166-1309")),
    person("Kavita", "Krishnan", role = c("aut"), email = "kkrishnan@jhmi.edu", comment = c(ORCID = "0000-0003-1345-0249")),
    person("Dmitrijs", "Lvovs", role = c("aut"), email = "dlvovs1@jhmi.edu"),
    person("Elana", "Fertig", role = "ctb", email = "ejfertig@jhmi.edu", comment = c(ORCID = "0000-0003-3204-342X")),
    person("Jennifer", "Elisseeff", role = "ctb", email = "jhe@jhu.edu", comment = c(ORCID = "0000-0002-5066-1996"))
    )
Description: 
    dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from cellphoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
BugReports: https://github.com/FertigLab/dominoSignal/issues
Depends:
    R(>= 4.2.0),
Imports:
    biomaRt,
    ComplexHeatmap,
    circlize,
    ggpubr,
    grDevices,
    grid,
    igraph,
    Matrix,
    methods,
    plyr,
    stats,
    utils
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.1
biocViews:
    SystemsBiology,
    SingleCell,
    Transcriptomics,
    Network
Suggests:
    knitr,
    patchwork,
    rmarkdown,
    Seurat,
    testthat,
    formatR,
    BiocFileCache,
    SingleCellExperiment
VignetteBuilder: knitr
Language: en-US
Roxygen: list(markdown = TRUE)
URL: https://fertiglab.github.io/dominoSignal/

[lshep]

Please see previous comments on initial submission. In summary:

vignette

• Please show things like options and set.seeds to users so they can
  accurately run and reproduce the code in the vignette.

• We don't allow data to be on github. can the data retrieved from github
  also be moved to a trusted site like zenodo.

• Vignette code must be executable. Currently no code is evaluated.

General

• There is currently no interop with Bioconductor standard classes for
  single cell. Please adjust package to also account for this and show
  examples. See SingleCellExperiment packages/class.

• Packages used in vignettes and examples must be on CRAN or Bioconductor.

It also appears the re-naming is not complete:

R CMD build dominoSignal 
* checking for file 'dominoSignal/DESCRIPTION' ... OK
* preparing 'dominoSignal':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘domino2.Rmd’ using rmarkdown

Quitting from lines  at lines 24-32 [libraries] (domino2.Rmd)
Error: processing vignette 'domino2.Rmd' failed with diagnostics:
there is no package called 'domino2'
--- failed re-building ‘domino2.Rmd’

[jmitchell81]

Hello @lshep. My apologies for this issues that were carried over from the last submission. We had an issue with our GitHub action for pushing development changes to this submission branch. I will have these resolved quickly.

To your point about data from GitHub, is this in regards points in the vignettes when data from the cellPhoneDB ligand-receptor database is downloaded from https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz ? This is data curated by another laboratory that we do not have permission to re-host on zenodo. We could use a toy data base for vignette examples if need be while directing to this data base resource in the documentation if we are not allowed to directly download from this source in the scripting of the vignette.

[lshep]

you can leave the github data for now and we can look into further in the review.

[jmitchell81]

Thank you @lshep. I have corrected our submission branch at HEAD. We're ready for your review.