submitting new package CatsCradle

[michaeldshapiro]

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• Repository: https://github.com/annaladdach/CatsCradle

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[bioc-issue-bot]

Hi @michaeldshapiro

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: CatsCradle
Title: This package discovers gene clusters in Seurat data
Version: 0.99.0
Authors@R:
    person(given = "Anna",
        family = "Laddach",
        role = c("aut", "cre"),
        email = "[email protected]",
        comment = c(ORCID = "0000-0001-5552-6534"))
    person(given = "Michael",
        family = "Shapiro",
        role = c("aut", "cre"),
        email = "[email protected]",
        comment = c(ORCID = "0000-0002-2769-9320"))
Description: The basic insight driving this package is the idea that by transposing the expression matrix of a Seurat object, we can use the usual Seurat technology to cluster genes and to visualise their relationships in two dimensions, e.g., as UMAP plots.  In addition we are then able to use the nearest neighbor graph to gain additional insight into specific genes by querying their neighborhood in this graph. 
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: Seurat,
	 ggplot2,
	 networkD3,
	 stringr,
	 pracma,
	 knitr,
	 reshape2,
	 rdist,
	 igraph,
	 interp,
	 geometry,
	 Rfast,
	 dplyr,
	 data.table,
	 abind,
	 pheatmap,
	 fossil
Depends: 
    R (>= 4.0)
LazyData: true
VignetteBuilder: knitr
LazyDataCompression: xz
biocViews:
    BiologicalQuestion,
    StatisticalMethod,
    GeneExpression,
    SingleCell,
    Transcriptomics

[lshep]

The docs directory should be removed. These documentations should be generated automatically with R CMD build.

Seurat objects are not Bioconductor objects. This package should be altered to additionally be able use the main Bioconductor object for expression matrix, SummarizedExperiment/SingleCellExperiment.

Please also be sure to run R CMD build, R CMD check and BiocCheck on the package.

> cellTypesPerCellType = computeCellTypesPerCellTypeMatrix(NBHDByCTMatrix,
+                                                      smallXenium$seurat_clusters)
Error in `x[[i, drop = TRUE]]`:
! ‘seurat_clusters’ not found in this Seurat object
 
Backtrace:
     ▆
  1. ├─CatsCradle::computeCellTypesPerCellTypeMatrix(...)
  2. │ ├─stats::aggregate(nbhdByCellType, list(cellTypes), sum)
  3. │ └─stats::aggregate.data.frame(...)
  4. ├─smallXenium$seurat_clusters
  5. └─SeuratObject:::`$.Seurat`(smallXenium, seurat_clusters)
  6.   ├─x[[i, drop = TRUE]]
  7.   └─SeuratObject:::`[[.Seurat`(x, i, drop = TRUE)
  8.     └─base::tryCatch(...)
  9.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.           └─value[[3L]](cond)
 12.             └─rlang::abort(...)

[michaeldshapiro]

We have pushed a new version of the package with the updated version number 0.99.1. We believe this version responds successfully to the suggestions. In particular, it now passes R CMD check and BiocCheck, and we have removed to doc folder.

We like the idea of enabling the package to work with, e.g., SingleCellExperiment objects. Functions which accept Seurat objects now also accept equivalent data in the form of a SingleCellExperiment of SpatialExperiment object. Similarly, functions which return as Seurat object can now return a SingleCellExperiment of SpatialExperiment at the user's request. This has been accomplished using adaptors that are only slightly deeper than, e.g., as.SingleCellExperiment. We have also provided expamples showing this capability.

We think this raises a larger question for the community. Seurat is an industry standard and will continue to evolve. We wonder if there oughtn't be a package which provides deeper conversions between Seurat and Bioconductor objects. This is beyond the scoper of CatsCradle and deserves to be treated as its own project.

Many thanks for your review of our work.

[lshep]

Agreed regarding Seurat/Bioc object conversion. https://satijalab.org/seurat/archive/v4.3/conversion_vignette looks like there was at least some effort to make some standardized conversions between objects; however I don't know how mature it is or if a deeper effort is being investigated.

[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
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WARNING should be granted an exception.

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[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

On one or more platforms, the build results were: "WARNINGS, ERROR".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): CatsCradle_0.99.1.tar.gz
macOS 12.7.1 Monterey: CatsCradle_0.99.1.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
[email protected]:packages/CatsCradle to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.