microRNAome

[mccallm]

• Repository: https://github.com/mccallm/microRNAome

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[bioc-issue-bot]

Hi @mccallm

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: microRNAome
Version: 0.99.0
Date: 2017-05-12
Title: SummarizedExperiment for the microRNAome project
Description: This package provides a SummarizedExperiment object of
        read counts for microRNAs across tissues, cell-types, and cancer cell-lines. 
    The read count matrix was prepared and provided by the author of the
        study: Towards the human cellular microRNAome.
Author: Matthew N. McCall <mccallm@gmail.com>, Marc K. Halushka <mhalush1@jhmi.edu>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
Depends: R (>= 3.4), SummarizedExperiment
Suggests: BiocGenerics, RUnit
biocViews: ExperimentData, CellCulture, CancerData, SequencingData, RNASeqData, miRNAData
License: GPL (>= 2)
URL: http://bioconductor.org

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

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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 Linux, Mac, and Windows.

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

Please see the following build report for more details:

http://bioconductor.org/spb_reports/microRNAome_buildreport_20170516075019.html

[vobencha]

Hi Matthew,

Looks like an experimental data package. A few suggestions below.

1. Explain the dimensions on the man page The man page says ... " New small RNA-seq data from 39 primary cells obtained by culture, flow cytometry or centrifugation were augmented with Sequence Read Archive (SRA) small RNA-seq read data from 496 samples with over 1 million microRNA reads. ..."

Explain how these numbers become 2131 and 528:

> dim(microRNAome)
[1] 2131  528

2. Add an \examples section that shows how to find the data. Explain that in this object the 'assays' only holds one matrix and the name is "counts" (vs an SE object that holds many matrices).

   > names(assays(microRNAome))
   [1] "counts"
   > assays(microRNAome)$counts[1:3,1:3]
                   SRR2296788 ERR738403 ERR738404
   hsa-let-7a-2-3p              0         0         0
   hsa-let-7a-3p               73        77        87
   hsa-let-7a-5p/7c-5p      71331     41863     43784

3. The URL field in DESCRIPTION usually refers to an external repo, e.g., github or someone's personal web site. I don't think it adds value to refer to the Bioconductor web site so I'd suggest removing this field.

4. Was this data package designed to work with an existing software package? If yes, you may want to mention that in the man page - you don't need an example with the software package, just a heads up to the users.

Valerie

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

e12ec86 Update microRNAome man page and DESCRIPTION

[mccallm]

Hi Valerie,

I made the suggested changes to the microRNAome.Rd and DESCRIPTION files.

This data package isn't designed to work with any specific software package.

Thanks, Matt

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, 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 following build report for more details:

http://bioconductor.org/spb_reports/microRNAome_buildreport_20170602120709.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

d9e781e Fix typo in microRNAome man page.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the following build report for more details:

http://bioconductor.org/spb_reports/microRNAome_buildreport_20170602122902.html

[vobencha]

Thanks for making the changes. Marking as approved. Valerie

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor svn repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

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