jazzPanda

[MelodyJIN-Y]

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

• Repository: https://github.com/phipsonlab/jazzPanda

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[bioc-issue-bot]

Hi @MelodyJIN-Y

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: jazzPanda
Type: Package
Title: Finding spatially relevant marker genes in image based spatial transcriptomics data 
Version: 0.99.0
Date: 2024-07-25
Authors@R: 
  c(person(given = "Melody",
 family = "Jin",
 role = c("aut", "cre"),
 email = "jin.m@wehi.edu.au",
 comment=c(ORCID="0000-0002-2222-0958"))
    )
LazyData: FALSE
Depends: R (>= 4.4.0)
Imports: spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr, doParallel, BiocParallel
VignetteBuilder: knitr
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    spatstat,
    Seurat,
    statmod,
    corrplot,
    ggplot2,
    ggraph,
    ggrepel,
    gridExtra,
    reshape2,
    igraph,
    jsonlite,
    vdiffr,
    patchwork,
    ggpubr,
    tidyr,
    data.table,
    testthat (>= 3.0.0)
Description: This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise. 
License: GPL-3 + file LICENSE
URL: https://github.com/phipsonlab/jazzPanda, https://bhuvad.github.io/jazzPanda/
BugReports: https://github.com/phipsonlab/jazzPanda/issues
biocViews: Spatial, GeneExpression, DifferentialExpression, StatisticalMethod, Transcriptomics
RoxygenNote: 7.3.2
Encoding: UTF-8
Config/testthat/edition: 3

[lshep]

Packages are generally expected to use standard Bioconductor class objects. Please expand to use standard class objects like SpatialExperiment or SingleCellExperiment. For What Its Worth you might also check out the Experiment Data Package TENxXeniumData that already provides Xenium data in such a standard class object.

[lshep]

May we expect updates soon?

[MelodyJIN-Y]

Hi, I am overseas and will make updates in 2 weeks. Apologies for the delay.

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.

[MelodyJIN-Y]

Hi, Thank you for your comments, and I apologize for the delay in updates.

• We have introduced a new function, convert_data, which converts data from the SingleCellExperiment, SpatialExperiment, and SpatialFeatureExperiment classes into a simple list format that can be directly passed to jazzPanda. We have included some examples in the vignette to aid with this new feature. We will continue to add support for other data classes as new ones emerge in the field of spatial data.

• We appreciate your suggestion regarding the TENxXeniumData/ExperimentHub package. Upon review, we found that the available datasets from TENxXeniumData and ExperimentHub do not include multi-sample examples that would demonstrate the full capabilities of our package.

[lshep]

Your package should take a SingleCellExperiment/SpatialExperiment class directly; it should not be flattened to a list and then used to create a Seurat object. Seurat objects are not valid Bioconductor class objects. You certainly can keep the interaction with Seurat but you should also make the package directly accept the standard Bioconductor class object (and ideally be endomorphic to return the same class object as output as input)

[MelodyJIN-Y]

Hi,

Thank you for your feedback. We have updated our package to accept SingleCellExperiment/SpatialExperiment/SpatialFeatureExperiment classes directly as input. This change aligns with Bioconductor standards and should improve user experience