Closed isarnassiri closed 6 years ago
Hi @isarnassiri
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: CMEA
Title: CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
Version: 0.99.0
Authors@R: c(person("Isar", "Nassiri", email = "isar_nassiri@urmc.rochester.edu", role = c("aut", "cre")))
Description: CMEA is a tool for cell morphology enrichment analysis and link transcriptomic alterations with cell morphological phenotypes. In our approach we (1) map the transcriptomic profile of a query against the L1000 LINCS repository, (2) create a gene set repository for cell morphological features (CM), (3) identify the top CMs associated with alterations and analyze their direction of regulation, and (4) model a regulatory network of cell morphological phenotypes.
Depends: R (>= 3.3.1), plotly, clusterSim, netbenchmark, qgraph, data.table, glmnet, PANR, Hmisc, caret, arules, arulesViz, vegan, ggplot2, gridExtra, plotrix, netbenchmark, igraph
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
biocViews: Software, StatisticalMethod, Regression
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-02 15:29:15 UTC; inassiri1
Author: Isar Nassiri [aut, cre], Matthew McCall [aut, cre]
Maintainer: Isar Nassiri <isar_nassiri@urmc.rochester.edu>
Your package has been approved for building. Your package is now submitted to our queue.
IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.
Hello,
I uploaded the CMEA package, including the complete repositories of cell morphology and transcriptomic profiles to the Github (https://github.com/isarnassiri/CMEA) through the Bitbucket.
I submitted the CMEA package to the Bioconductor.
Best regards, Isar
From: bioc-issue-bot [mailto:notifications@github.com] Sent: Friday, April 07, 2017 8:49 PM To: Bioconductor/Contributions Cc: Nassiri, Isar; Mention Subject: Re: [Bioconductor/Contributions] CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile (#344)
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: CMEA
Title: CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile
Version: 0.99.0
Authors@R: c(person("Isar", "Nassiri", email = "isar_nassiri@urmc.rochester.edumailto:isar_nassiri@urmc.rochester.edu", role = c("aut", "cre")))
Description: CMEA is a tool for cell morphology enrichment analysis and link transcriptomic alterations with cell morphological phenotypes. In our approach we (1) map the transcriptomic profile of a query against the L1000 LINCS repository, (2) create a gene set repository for cell morphological features (CM), (3) identify the top CMs associated with alterations and analyze their direction of regulation, and (4) model a regulatory network of cell morphological phenotypes.
Depends: R (>= 3.3.1), plotly, clusterSim, netbenchmark, qgraph, data.table, glmnet, PANR, Hmisc, caret, arules, arulesViz, vegan, ggplot2, gridExtra, plotrix, netbenchmark, igraph
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1.9000
biocViews: Software, StatisticalMethod, Regression
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-02 15:29:15 UTC; inassiri1
Author: Isar Nassiri [aut, cre], Matthew McCall [aut, cre]
Maintainer: Isar Nassiri isar_nassiri@urmc.rochester.edu<mailto:isar_nassiri@urmc.rochester.edu>
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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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170407211958.html
Hello, I revised the code, and fixed the warnings. I have pushed the code to git. Best regards, Isar
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170419133721.html
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170419193859.html
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170419193931.html
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170420091133.html
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170420115928.html
Received a valid push; starting a build. Commits are:
72c4bea Add files via upload
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170420122644.html
Received a valid push; starting a build. Commits are:
35d724b Add files via upload Revised.
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170420131315.html
Hello,
The "WARNINGS" is " 'rgl_init' failed, running with rgl.useNULL = TRUE", and is a problem with the build system itself.
Best regards, Isar
Hi Isar,
Thanks for submitting the CMEA package. Please take the time to read carefully our package guidelines here. CMEA fails to satisfy 2 important criteria from these guidelines: it's too big and the vignette has no real code chunks. Also, the package has usability issues that are so severe that it's almost impossible for me to test it and judge its usefulness. Overall it will need a lot of work to reach an acceptable level. See details below.
Regards, H.
Package is too big: 73M. That's because it contains big data sets of experimental data. The source tarball of a Bioconductor software package should occupy less than 4MB on disk. Please check our package guidelines (at https://bioconductor.org/developers/package-guidelines/) and make sure CMEA satisfies them. One way to reduce the size is to move all the experimental data to a separate data experiment package. Let's call this solution 1. If the data is not too big, another way to reduce the size of the package is to explicitly download the data in the examples or vignette. Let's call this solution 2.
Your data sets are poorly documented. We need to know exactly where the data is coming from and how it was retrieved. For example the man page for Cell_Morphology_Profile
only says that the data comes from the LINCS database but it doesn't say what data it is exactly from this database or how it was extracted from it. Also the man page doesn't say what the row names of the data frame are. So if you opt for solution 1, make sure the data sets are well documented in the data experiment package. If you opt for solution 2, then things will be more transparent and reproducible because you'll provide the code for downloading the data sets. Even if you opt for solution 1, I would strongly suggest that you make available the code you used to generate the data sets in the data experiment package.
Your vignette doesn't contain any real code chunks i.e. code chunks that are evaluated by R CMD build
. This is called a static vignette. Bioconductor vignettes should never be static i.e. they must contain real code chunks. See our package guidelines for more information on this.
None of your functions have arguments. The input they take is unclear. Some of it seems to come from some user defined variables (e.g. number_of_features
for Cell_Morphology_Enrichment_Analysis()
). But they also seem to take as input some files produced by other functions. This is very poor software design. Besides, none of this is documented. This makes the package barely usable.
One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features()
function:
> library(CMEA)
> example(Ranking_Cell_Morphological_features)
R_C_M_> {
R_C_M_+ data(Transcriptomic_Profile)
R_C_M_+ data(Cell_Morphology_Profile)
R_C_M_+ TOP=20
R_C_M_+ Ranking_Cell_Morphological_features()
R_C_M_+ }
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt':
No such file or directory
That's probably because it requires other things from other examples to run before it. All the examples should work independently from each others.
Some of your functions (e.g. Cell_Morphology_Enrichment_Analysis()
) write their output to the package installation folder. This is a very bad idea. The package installation folder should always be treated as a read-only place.
Please use camelCase style for your function names e.g. crossTabulation()
instead of crosstabulation()
or rankCellMorphologicalFeatures()
instead of Ranking_Cell_Morphological_features()
etc... (Also note that you could use "rank" instead of "ranking".)
The examples provided in the man pages are all inside curly brackets ({
... }
). These curly brackets have no purpose and should be removed.
Use <-
instead of =
for assignments.
Received a valid push; starting a build. Commits are:
e3b5811 Add files via upload
Received a valid push; starting a build. Commits are:
ef83dfc Revised.
Received a valid push; starting a build. Commits are:
e5c0286 R.
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170613155321.html
Received a valid push; starting a build. Commits are:
59fa2b4 Revised.
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170613165922.html
Received a valid push; starting a build. Commits are:
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170614164030.html
Received a valid push; starting a build. Commits are:
8058bde Revised.
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170614180949.html
Received a valid push; starting a build. Commits are:
7a394d4 Revised.
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170614184324.html
Received a valid push; starting a build. Commits are:
84898b1 Revised.
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170616153246.html
Received a valid push; starting a build. Commits are:
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170616154242.html
Received a valid push; starting a build. Commits are:
18322a0 Revised.
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170617140505.html
Received a valid push; starting a build. Commits are:
Received a valid push; starting a build. Commits are:
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170619161235.html
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, 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 following build report for more details:
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Hello,
I am pleased to resubmit the revised version of CMEA package. I appreciated the constructive criticisms of the reviewer. I have addressed each of his concerns as outlined below.
We moved the files of complete experimental data to a separate data experiment package, and used subset of the complete dataset as an example input. The package size now is 2.22MB.
The input data were explained in vignette/documents with more details. We explained the origin of data with proper citations.
We added some real code chunks to the vignette, and improved it thoroughly.
The name of the functions were revised. We added arguments with comprehensive explanations. All functions return the R objects in the global environment after running them.
One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features() function:
library(CMEA)
example(Ranking_Cell_Morphological_features)
R_CM> {
R_CM+ data(Transcriptomic_Profile)
R_CM+ data(Cell_Morphology_Profile)
R_CM+ TOP=20
R_CM+ Ranking_Cell_Morphological_features()
R_CM+ }
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt':
No such file or directory
That's probably because it requires other things from other examples to run before it. All the examples should work independently.
Revised. All the examples work independently, and return the R objects in the global environment after running them.
Revised. All functions return their outputs to the global environment.
Thanks for the comment. We used CamelCase symbol names for function names.
Unessential curly brackets in the man pages were removed.
Revised. Best regards, Isar
From: hpages [mailto:notifications@github.com] Sent: Thursday, May 25, 2017 3:11 AM To: Bioconductor/Contributions Cc: Nassiri, Isar; Manual Subject: Re: [Bioconductor/Contributions] CMEA: An R Package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile (#344)
Hi Isar,
Thanks for submitting the CMEA package. Please take the time to read carefully our package guidelines here . CMEA fails to satisfy 2 important criteria from these guidelines: it's too big and the vignette has no real code chunks. Also, the package has usability issues that are so severe that it's almost impossible for me to test it and judge its usefulness. Overall it will need a lot of work to reach an acceptable level. See details below.
Regards, H.
Package is too big: 73M. That's because it contains big data sets of experimental data. The source tarball of a Bioconductor software package should occupy less than 4MB on disk. Please check our package guidelines (at ) and make sure CMEA satisfies them. One way to reduce the size is to move all the experimental data to a separate data experiment package. Let's call this solution 1. If the data is not too big, another way to reduce the size of the package is to explicitly download the data in the examples or vignette. Let's call this solution 2.
Your data sets are poorly documented. We need to know exactly where the data is coming from and how it was retrieved. For example the man page for Cell_Morphology_Profile only says that the data comes from the LINCS database but it doesn't say what data it is exactly from this database or how it was extracted from it. Also the man page doesn't say what the row names of the data frame are. So if you opt for solution 1, make sure the data sets are well documented in the data experiment package. If you opt for solution 2, then things will be more transparent and reproducible because you'll provide the code for downloading the data sets. Even if you opt for solution 1, I would strongly suggest that you make available the code you used to generate the data sets in the data experiment package.
Your vignette doesn't contain any real code chunks i.e. code chunks that are evaluated by R CMD build. This is called a static vignette. Bioconductor vignettes should never be static i.e. they must contain real code chunks. See our package guidelines for more information on this.
None of your functions have arguments. The input they take is unclear. Some of it seems to come from some user defined variables (e.g. number_of_features for Cell_Morphology_Enrichment_Analysis()). But they also seem to take as input some files produced by other functions. This is very poor software design. Besides, none of this is documented. This makes the package barely usable.
One consequence of this design is that I can't run the example in the man page of the Ranking_Cell_Morphological_features() function:
library(CMEA)
example(Ranking_Cell_Morphological_features)
R_CM> {
R_CM+ data(Transcriptomic_Profile)
R_CM+ data(Cell_Morphology_Profile)
R_CM+ TOP=20
R_CM+ Ranking_Cell_Morphological_features()
R_CM+ }
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/hpages/R/R-3.4.r72630/library/CMEA/TP_subset.txt':
No such file or directory
That's probably because it requires other things from other examples to run before it. All the examples should work independently from each others.
Some of your functions (e.g. Cell_Morphology_Enrichment_Analysis()) write their output to the package installation folder. This is a very bad idea. The package installation folder should always be treated as a read-only place.
Please use camelCase style for your function names e.g. crossTabulation() instead of crosstabulation() or rankCellMorphologicalFeatures() instead of Ranking_Cell_Morphological_features() etc... (Also note that you could use "rank" instead of "ranking".)
The examples provided in the man pages are all inside curly brackets ({ ... }). These curly brackets have no purpose and should be removed.
Use <- instead of = for assignments.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_344-23issuecomment-2D303940596&d=DQMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E-oniHbGv_UHjPSrRjRIX5Oxoyh1VH3wE7UxwyHhNAU&m=VNwnu3ifhoMH11S9EcvassHvsZKfMWH93SY0skQp408&s=9kQbxnXX52dgmJ3l98Hkt43SP1Yx7g3p6xuFe63JztM&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AZxqFbXatMHJWXfUzl-5FV86DwkSbOAFqkks5r9SlvgaJpZM4M3iZG&d=DQMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E-oniHbGv_UHjPSrRjRIX5Oxoyh1VH3wE7UxwyHhNAU&m=VNwnu3ifhoMH11S9EcvassHvsZKfMWH93SY0skQp408&s=m8Lb0igpOYxBh874tEMX2yzBexS70sD3HhIjRd4a7hc&e=.
Received a valid push; starting a build. Commits are:
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, 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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170621094451.html
Received a valid push; starting a build. Commits are:
5b6a512 Revised.
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170621095637.html
Received a valid push; starting a build. Commits are:
1c0ba9b Revised.
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 following build report for more details:
http://bioconductor.org/spb_reports/CMEA_buildreport_20170624120925.html
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