Closed const-ae closed 3 years ago
Hi @const-ae
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: transformGamPoi
Type: Package
Title: Variance Stabilizing Transformation for Gamma-Poisson Models
Version: 0.99.0
Authors@R: person("Constantin", "Ahlmann-Eltze", email = "artjom31415@googlemail.com",
role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3762-068X"))
Description: Variance-stabilizing transformations help with the analysis of
heteroskedastic data (i.e., data where the variance is not constant, like count data).
This package provide two types of variance stabilizing transformations: (1) methods based on the
delta method (e.g., 'acosh', 'log(x+1)'), (2) model residual based (Pearson and randomized
quantile residuals).
BugReports: https://github.com/const-ae/transformGamPoi/issues
URL: https://github.com/const-ae/transformGamPoi
License: GPL-3
Encoding: UTF-8
Imports:
glmGamPoi,
DelayedArray,
Matrix,
MatrixGenerics,
SummarizedExperiment,
HDF5Array,
methods,
utils
Suggests:
testthat,
TENxPBMCData,
scran,
knitr,
rmarkdown
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Config/testthat/edition: 3
biocViews: SingleCell, VarianceStabilization, Normalization, Regression
VignetteBuilder: knitr
Hi,
BiocCheck
currently detects 1 Warning and 6 Notes:
The warning concerns the biocViews
term 'VarianceStabilization'. I am aware that this is not in the list of biocTerms; however, I would like to suggest adding it. There are already three Bioconductor packages dedicated to this topic: vsn, lumi, and flowVS. If however, that is not possible I can of course also remove that term again.
[2] " Avoid redundant 'stop' and 'warn*' in signal conditions"
I assume this refers to rethrowing an error inside a tryCatch()
. I don't quite understand why this is problematic. I call a function from a separate package that sometimes fails. I want to give the user additional information about what happened and what the alternatives are without automatically picking an alternative for the user. Is there a better way to achieve this?
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
@const-ae VarianceStabilization is not a valid biocViews term. Please remove from the list of biocViews in the description
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: "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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/transformGamPoi
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 50081512a00090d3f215ba69221e424a026747f4
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 build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/transformGamPoi
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
VarianceStabilization is not a valid biocViews term. Please remove from the list of biocViews in the description
@lshep, okay. Done.
Hi @const-ae , @wolfganghuber, @lshep ,
Should we add VarianceStabilization
to the biocViews vocabulary? I see that we have a few other Bioconductor packages that provide tools for variance stabilization (vsn, lumi, flowVS, pmp, blima, etc...). Would be nice to be able to group them under a common view.
The name of the package (transformGamPoi) is made of a verb + an object. About the verb: so the package provides tools to transform Gamma Poisson Data. Note that there are many ways to transform data but the package specifically provides variance stabilizing transformations. Why not use a more specific name like GamPoiVS? About the object: I can see that using "GamPoi" to describe the type of data that the package is dealing with avoids implying that the package only applies to single cell data, but it also makes the name slightly more cryptic than necessary.
Anyways, these are minor concerns and none of this matters if the package can easily be found under the VarianceStabilization
and SingleCell
views. So this is maybe one more reason to support the VarianceStabilization
term?
Thanks, H.
Hi Hervé
Thank you.
A VarianceStabilization term seems to fine-grained to me, I’d probably prefer Preprocessing.
But who uses search by Keywords…? This sounds like Yahoo.com in 1998… At least in my experience, “everyone” is used to full text search (e.g. Google, Amazon, Netflix), and/or recommender systems that would suggest similar packages. So I’d rather make sure that many of the relevant keywords are in the package description and perhaps also in man pages and vignettes, and that these are text-mined and indexed for a clustering and search engine.
Agree with you that mnemonic, easily rememberable, descriptive package names are desirable and that the one in question is not really there yet.
Kind regards Wolfgang
Il giorno 14set2021, alle ore 19:22, Hervé Pagès @.***> ha scritto:
Hi @const-ae , @wolfganghuber, @lshep ,
Should we add VarianceStabilization to the biocViews vocabulary? I see that we have a few other Bioconductor packages that provide tools for variance stabilization (vsn, lumi, flowVS, pmp, blima, etc...). Would be nice to be able to group them under a common view.
The name of the package (transformGamPoi) is made of a verb + an object. About the verb: so the package provides tools to transform Gamma Poisson Data. Note that there are many ways to transform data but the package specifically provides variance stabilizing transformations. Why not use a more specific name like GamPoiVS. About the object: I can see that using GamPoi to describe the type of data that the package is dealing with avoids implying that the package only applies to single cell data, but it also makes the name slightly more cryptic than necessary.
Anyways, these are minor concerns and none of this matters if the package can easily be found under the VarianceStabilization and SingleCell views. So this is maybe one more reason to support the VarianceStabilization term?
Thanks, H.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.
Hi sorry for the silence.
The name of the package (transformGamPoi) is made of a verb + an object. About the verb: so the package provides tools to transform Gamma Poisson Data. Note that there are many ways to transform data but the package specifically provides variance stabilizing transformations. Why not use a more specific name like GamPoiVS? About the object: I can see that using "GamPoi" to describe the type of data that the package is dealing with avoids implying that the package only applies to single cell data, but it also makes the name slightly more cryptic than necessary.
Yeah, tbh I am not super happy with the name either. My thought process for choosing transformGamPoi is that the verb relates to sctransform which is closely related to my package. The noun GamPoi is indeed partially motivated to not just limited the application to single-cell data. However, the bigger motivation is to stay consistent with my other package glmGamPoi as they follow a similar philosophy.
A VarianceStabilization term seems to fine-grained to me, I’d probably prefer Preprocessing.
I added Preprocessing as a term
Thanks guys for explaining.
I realize now that the Preprocessing
and Normalization
views (which are both under the WorkflowStep
view) are leaf views. This suggests that adding VarianceStabilization
as a subview of Preprocessing
would take us to a level of refinement that we are not used too, so maybe not this time.
Otherwise the package looks good, thanks!
Cheers, H.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
The master branch of your GitHub repository has been added to Bioconductor's git repository.
To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/const-ae.keys is not empty), then no further steps are required. Otherwise, do the following:
See further instructions at
https://bioconductor.org/developers/how-to/git/
for working with this repository. See especially
https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
to keep your GitHub and Bioconductor repositories in sync.
Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at
https://bioconductor.org/checkResults/
(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("transformGamPoi")
. The package 'landing page' will be created at
https://bioconductor.org/packages/transformGamPoi
If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.