oob

[DimitriMeistermann]

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• Repository: https://github.com/DimitriMeistermann/oob

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[bioc-issue-bot]

Hi @DimitriMeistermann

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: oob
Type: Package
Title: oob: a toolbox for analyzing OMIC data, Out Of Bounds from any black box
Version: 0.99.0
Authors@R: person("Dimitri", "Meistermann", email = "[email protected]",role = c("aut", "cre"), comment=c(ORCID="0000-0001-6614-2325"))
Description: A toolbox for analyzing OMIC data, Out Of Bounds from any black box by avoiding the use of complex objects.
    This package provide function for analyzing OMIC data, with a focus on plots and bulk/single-cell RNA-Seq.
    In addition of providing diverse wrappers and utilities to ease the use of R with large datsets, it contains several unique features.
    Among them, the TRIMAP dimension reduction implementated with reticulate and tools for enriching intersection of gene lists.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
biocViews:
	Software,
	ResearchField,
	Transcriptomics,
	Clustering,
	DimensionReduction
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Depends: 
    R (>= 4.4.0),
    ggplot2,
    stats,
    ComplexHeatmap
Imports:
    basilisk,
    batchelor,
    BiocParallel,
    BiocGenerics,
    circlize,
    data.table,
    dbscan,
    ggbeeswarm,
    ggrepel,
    glmnet,
    grDevices,
    grid,
    irlba,
    labeling,
    lsa,
    MASS,
    Matrix,
    pvclust,
    reshape2,
    reticulate,
    rgl,
    Rcpp,
    RcppArmadillo,
    rlang,
    scales,
    scater,
    scattermore,
    scran,
    SingleCellExperiment,
    SummarizedExperiment,
    stringr,
    cli,
    uwot,
    graphics,
    methods,
    utils
Suggests: 
    knitr,
    rmarkdown,
    qualpalr,
    WGCNA
VignetteBuilder:  knitr
LinkingTo:
    Rcpp,
    RcppArmadillo
URL: https://github.com/DimitriMeistermann/oob
BugReports: https://github.com/DimitriMeistermann/oob/issues
StagedInstall: no

[lshep]

This package also need to interact with standard Bioconductor class structures for OMICs data like SummarizedExperiment/SingleCellExperiment.

[DimitriMeistermann]

Hi,
Thank you for your feedback.
I will add this week the support for SummarizedExperiment/SingleCellExperiment objects where I think it is relevant.

[DimitriMeistermann]

I updated the package to support SummarizedExperiment/SingleCellExperiment objects for the following functions:

• getMostVariableGenes
• getMarkers
• getMarkerGLMnet
• heatmap.DM
• plotExpr
• CPM
• TPMfullLength
• RPKM
• computeQCmetricSamples
• normDeseq
• oobFastMNN
• pcaAddSamples
• PCA
• fastPCA
• UMAP
• TRIMAP
• NMDS
• leidenFromUMAP
• pca2d
• proj2d

Thank you for your patience.

[lshep]

I'm getting the following ERROR when trying to build locally:

R CMD build oob 
* checking for file 'oob/DESCRIPTION' ... OK
* preparing 'oob':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'oob' ...
** using non-staged installation via StagedInstall field
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing '/tmp/RtmpxNKJWP/Rinst6d496204304/oob'
      -----------------------------------
ERROR: package installation failed

[DimitriMeistermann]

The problem should be resolved now, I apologize for this issue..

[lshep]

• I'm still getting the above ERROR

R CMD build oob 
* checking for file 'oob/DESCRIPTION' ... OK
* preparing 'oob':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'oob' ...
** using non-staged installation via StagedInstall field
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing '/tmp/RtmpxNKJWP/Rinst6d496204304/oob'
      -----------------------------------
ERROR: package installation failed

I changed locally to executable and ran build/check but I think you need to
change the permission on the files and recommit them.

• Note the size of package should be reduced. It is rather large and above
  the size requirement for Bioconductor. You'll be able to do some with the R
  CMD Check recommendation

* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                       old_size new_size compress
  bulkLogCounts.rda       4.0Mb    2.6Mb       xz
  geneLengthGRCh38.rda    166Kb    124Kb    bzip2
  humanGeneIDtable.rda    1.2Mb    411Kb       xz

I'll move the package forward to see if it happens on the daily builder too.

[bioc-issue-bot]

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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: "skipped, 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:
ERROR before build products produced.

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/oob to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 61b5448dbb3580f1593ee663bea18474b99820df

[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: "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 24.04.1 LTS): oob_0.99.2.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/oob to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 104f11cb8000b10377dcfcf190e2d75522a2fa61

[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".
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 24.04.1 LTS): oob_0.99.21.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/oob to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 8e5fcd7a62796ec8bbea882c4d3988aa93ae14cb

[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.

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 Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): oob_0.99.22.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/oob 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.

[vjcitn]

Thanks for your submission. The review will take some time, and I would like to start things off with some questions.

First, what is meant by "out of bounds"? You should explain this in the vignette and in the DESCRIPTION. The
DESCRIPTION suggests that "avoiding complex objects" is a key distinction. Why is this advantageous? Are
there new risks engendered by separating metadata from quantifications? SummarizedExperiment and derivates
have a long history of successful use for many tasks. What is the benefit of "avoiding complexity"? What is meant
by "any black box"?

Second, in the vignette we have:

When set `set.seed` is used the Random Number Generator give a different result
each time it is used. `getRandState`, `setRandState` are used for
retrieving/setting this precise seed state.

Why is new code needed for this? .Random.seed can be obtained directly for this purpose.

Third, with

Eventually, oobFastMNN can be used to perform a quick batch correction with the simple one matrix in, one matrix out format. ## Principal Component Analysis tools Principal Component Analysis can be performed with PCA or approximated with fastPCA with parameters optimized by default for RNA-Seq. Result can be then plotted with pca2d.

I would imagine that you are finding better throughput than existing methods in the sc-RNA-seq provided by
scater, scran, scuttle and so forth. Can you document the advantages in your vignette with e.g. microbenchmark
so that we have some context for understanding the role of these new components.

Thanks