Re: [Bioc-devel] Updating bioconductor after computer transfer - problem

[Turaga, Nitesh]

Hi Chris,

We have a key already for you. It is possible you are using the wrong key to 
access git.bioconductor.org. 

ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCv4h33vFVuXjQqddBgjU2398YglnXpOPL1xgU1t63JQ+bJWOQx2wl

That is the prefix of the key we have on file for you. One way is to submit a 
new key, if you don’t have access to the private key corresponding to your 
public key. You should have access once that new key is in our system. 

Best

Nitesh

> On Dec 15, 2017, at 2:06 AM, Christopher John  
> wrote:
> 
> Hi
> 
> I have recently copy and pasted my github directory from my old PC to a new
> PC. I can update the github still fine, but bioconductor I get an error:
> 
> christopher@RA-MAP:~/M3C$ git remote -v
> originhttps://github.com/crj32/M3C (fetch)
> originhttps://github.com/crj32/M3C (push)
> upstreamg...@git.bioconductor.org:packages/M3C.git (fetch)
> upstreamg...@git.bioconductor.org:packages/M3C.git (push)
> 
> .. the usual commands
> 
> christopher@RA-MAP:~/M3C$ git push origin master
> Username for 'https://github.com': crj32
> Password for 'https://cr...@github.com':
> Everything up-to-date
> 
> christopher@RA-MAP:~/M3C$ git push upstream master
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> I guessed this was to do with the ssh key not being update to date with the
> one from the new PC. So I followed the directions on this site and got my
> local ssh key, added it to the github, then sent the ssh key off to the
> bioconductor through the google forms page. Still no luck, same error. Was
> this the correct thing to do?
> 
> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
> 
> Thanks,
> 
> Chris
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] GSE62944, empty EH164 and EH165

[Shepherd, Lori]

Thank you for bringing this to our attention.


The resources were created with a previous version of SummarizedExperiment that 
were not compatible with the current version.


New resources have been added and are visible in both release 3.6 and devel 
3.7. Please note the new EH_id's:



> library(ExperimentHub)

> hub <- ExperimentHub()
snapshotDate(): 2017-10-30
> gse <- AnnotationHub::query(hub, "GSE62944")
> gse
ExperimentHub with 3 records
# snapshotDate(): 2017-10-30
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: SummarizedExperiment, ExpressionSet
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["EH1"]]'

   title
  EH1| RNA-Sequencing and clinical data for 7706 tumor samples from The...
  EH1043 | RNA-Sequencing and clinical data for 9246 tumor samples from The...
  EH1044 | RNA-Sequencing and clinical data for 741 normal samples from The...

> x = gse[["EH1043"]]
> x
class: SummarizedExperiment
dim: 23368 9264
metadata(0):
assays(1): CancerRaw
rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR
rowData names(0):
colnames(9264): TCGA-G9-A9S0-01A-11R-A41O-07
  TCGA-E1-5318-01A-01R-1470-07 ... TCGA-A7-A0DC-01A-11R-A00Z-07
  TCGA-A5-A0VQ-01A-11R-A104-07
colData names(549): bcr_patient_uuid bcr_patient_barcode ...
  lymph_nodes_aortic_pos_total CancerType
> dim(x)
[1] 23368  9264


> x = gse[["EH1044"]]
> x
class: SummarizedExperiment
dim: 23368 741
metadata(0):
assays(1): NormalRaw
rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR
rowData names(0):
colnames(741): TCGA-K4-A3WV-11A-21R-A22U-07
  TCGA-49-6742-11A-01R-1858-07 ... TCGA-BH-A0H5-11A-62R-A115-07
  TCGA-22-5489-11A-01R-1635-07
colData names(2): sample type
> dim(x)
[1] 23368   741


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Ludwig 
Geistlinger 
Sent: Thursday, December 14, 2017 3:01:56 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] GSE62944, empty EH164 and EH165

Hi,


I'm trying to obtain the most recent version of GSE62944 from ExperimentHub via


> library(ExperimentHub)

> hub <- ExperimentHub()

> gse <- AnnotationHub::query(hub, "GSE62944")


> gse
ExperimentHub with 3 records
# snapshotDate(): 2017-10-30
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: SummarizedExperiment, ExpressionSet
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["EH1"]]'

  title
  EH1   | RNA-Sequencing and clinical data for 7706 tumor samples from The...
  EH164 | RNA-Sequencing and clinical data for 9246 tumor samples from The...
  EH165 | RNA-Sequencing and clinical data for 741 normal samples from The...


Retrieving the original (outdated) dataset works fine:

> x <- gse[["EH1"]]

> dim(x)
Features  Samples
   23368 7706


However,  obtaining the most recent version of the data via


> x <- gse[["EH164"]]


gives me:


> dim(x)
NULL


> class(x)
[1] "SummarizedExperiment0"
attr(,"package")
[1] "SummarizedExperiment"

> str(x)
Formal class 'SummarizedExperiment0' [package "SummarizedExperiment"] with 0 
slots
 Named list()


It would be great if this could be updated.


Thanks a lot,

Ludwig


--
Dr. Ludwig Geistlinger
CUNY School of Public Health



> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] SummarizedExperiment_1.8.0 DelayedArray_0.4.1
 [3] matrixStats_0.52.2 GenomicRanges_1.30.0
 [5] GenomeInfoDb_1.14.0IRanges_2.12.0
 [7] S4Vectors_0.16.0   GSE62944_1.6.0
 [9] GEOquery_2.46.8Biobase_2.38.0
[11] ExperimentHub_1.4.0AnnotationHub_2.10.1
[13] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14  XVector_0.18.0
 [3] BiocInstaller_1.28.0  compiler_3.4.2
 [5] bindr_0.1 zlibbioc_1.24.0
 [7] bitops_1.0-6  tools_3.4.2
 [9] digest_0.6.12 bit_1.1-12
[11] lattice_0.20-35   RSQLite_2.0
[13] memoise_1.1.0 tibble_1.3.4
[15] pkgconfig_2.0.1   rlang_0.1.4
[17] Matrix_1.2-12 

Re: [Bioc-devel] GSE62944, empty EH164 and EH165

[Ludwig Geistlinger]

Great! Thanks for resolving this so fast. Ludwig



From: Shepherd, Lori 
Sent: Friday, December 15, 2017 1:48 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: GSE62944, empty EH164 and EH165


Thank you for bringing this to our attention.


The resources were created with a previous version of SummarizedExperiment that 
were not compatible with the current version.


New resources have been added and are visible in both release 3.6 and devel 
3.7. Please note the new EH_id's:



> library(ExperimentHub)

> hub <- ExperimentHub()
snapshotDate(): 2017-10-30
> gse <- AnnotationHub::query(hub, "GSE62944")
> gse
ExperimentHub with 3 records
# snapshotDate(): 2017-10-30
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: SummarizedExperiment, ExpressionSet
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["EH1"]]'

   title
  EH1| RNA-Sequencing and clinical data for 7706 tumor samples from The...
  EH1043 | RNA-Sequencing and clinical data for 9246 tumor samples from The...
  EH1044 | RNA-Sequencing and clinical data for 741 normal samples from The...

> x = gse[["EH1043"]]
> x
class: SummarizedExperiment
dim: 23368 9264
metadata(0):
assays(1): CancerRaw
rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR
rowData names(0):
colnames(9264): TCGA-G9-A9S0-01A-11R-A41O-07
  TCGA-E1-5318-01A-01R-1470-07 ... TCGA-A7-A0DC-01A-11R-A00Z-07
  TCGA-A5-A0VQ-01A-11R-A104-07
colData names(549): bcr_patient_uuid bcr_patient_barcode ...
  lymph_nodes_aortic_pos_total CancerType
> dim(x)
[1] 23368  9264


> x = gse[["EH1044"]]
> x
class: SummarizedExperiment
dim: 23368 741
metadata(0):
assays(1): NormalRaw
rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR
rowData names(0):
colnames(741): TCGA-K4-A3WV-11A-21R-A22U-07
  TCGA-49-6742-11A-01R-1858-07 ... TCGA-BH-A0H5-11A-62R-A115-07
  TCGA-22-5489-11A-01R-1635-07
colData names(2): sample type
> dim(x)
[1] 23368   741


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Ludwig 
Geistlinger 
Sent: Thursday, December 14, 2017 3:01:56 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] GSE62944, empty EH164 and EH165

Hi,


I'm trying to obtain the most recent version of GSE62944 from ExperimentHub via


> library(ExperimentHub)

> hub <- ExperimentHub()

> gse <- AnnotationHub::query(hub, "GSE62944")


> gse
ExperimentHub with 3 records
# snapshotDate(): 2017-10-30
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: SummarizedExperiment, ExpressionSet
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["EH1"]]'

  title
  EH1   | RNA-Sequencing and clinical data for 7706 tumor samples from The...
  EH164 | RNA-Sequencing and clinical data for 9246 tumor samples from The...
  EH165 | RNA-Sequencing and clinical data for 741 normal samples from The...


Retrieving the original (outdated) dataset works fine:

> x <- gse[["EH1"]]

> dim(x)
Features  Samples
   23368 7706


However,  obtaining the most recent version of the data via


> x <- gse[["EH164"]]


gives me:


> dim(x)
NULL


> class(x)
[1] "SummarizedExperiment0"
attr(,"package")
[1] "SummarizedExperiment"

> str(x)
Formal class 'SummarizedExperiment0' [package "SummarizedExperiment"] with 0 
slots
 Named list()


It would be great if this could be updated.


Thanks a lot,

Ludwig


--
Dr. Ludwig Geistlinger
CUNY School of Public Health



> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
 [1] SummarizedExperiment_1.8.0 DelayedArray_0.4.1
 [3] matrixStats_0.52.2 GenomicRanges_1.30.0
 [5] GenomeInfoDb_1.14.0IRanges_2.12.0
 [7] S4Vectors_0.16.0   GSE62944_1.6.0
 [9] GEOquery_2.46.8Biobase_2.38.0
[11] ExperimentHub_1.4.0AnnotationHub_2.10.1
[13] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14  XVector_0.18.0
 [3] BiocInstaller_1.28.0  compiler_3.4.2
 [5] bindr_0.1  

Re: [Bioc-devel] git push to Bioconductor failing

[Turaga, Nitesh]

Hi Gabriel,

You seem to have not submitted your SVN ID. Please submit your key along with 
that information.

Best

Nitesh 

> On Dec 15, 2017, at 12:50 PM, Hoffman, Gabriel  
> wrote:
> 
> Hi,
> 
> I am having an issue pushing changes from my git repo to Bioconductor.  I can 
> push changes to Github just fine.
> 
> 
> Here my push command fails.
> 
> 
>> git push upstream
> 
> FATAL: W any packages/variancePartition gabrielhoffman DENIED by fallthru
> 
> (or you mis-spelled the reponame)
> 
> fatal: Could not read from remote repository.
> 
> 
> Please make sure you have the correct access rights
> 
> and the repository exists.
> 
> I have the proper upstream location set
> 
> 
>> git remote -v
> 
> origin https://github.com/GabrielHoffman/variancePartition.git (fetch)
> 
> origin https://github.com/GabrielHoffman/variancePartition.git (push)
> 
> upstream g...@git.bioconductor.org:packages/variancePartition (fetch)
> 
> upstream g...@git.bioconductor.org:packages/variancePartition (push)
> 
> 
> But it seems like I don't have write access to this repo.
> 
> 
>> ssh -T g...@git.bioconductor.org | grep variancePartition
> 
> R  packages/variancePartition
> 
> 
> 
> I have registered my SSH RSA key with Bioconductor, and I have received the 
> emails saying it was approved.  But I still do not have write access.
> 
> 
> Do you have any suggestions to debug this?
> 
> 
> Thanks,
> 
> - Gabriel
> 
> 
> 
> 
> --
> 
> Gabriel Hoffman, Ph.D.
> 
> 
> 
> Assistant Professor
> 
> Icahn Institute for Genomics and Multiscale Biology
> 
> Department of Genetics and Genomic Sciences
> 
> Icahn School of Medicine at Mount Sinai
> 
> 
> 
> gabriel.hoff...@mssm.edu
> 
> 
> 
> 1425 Madison Avenue
> 
> New York, NY 10029
> 
> Icahn Building L3-70B
> 
> 212-659-1635
> 
> 
> http://gabrielhoffman.github.io
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

[Ludwig Geistlinger]

Hi Lori,

I would be willing to take over maintenance of 

ToPASeq

in case maintainers remain unresponsive.

Best,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Friday, December 15, 2017 9:29 AM
To: Martin Morgan
Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly.

The current list of deprecated packages is as follows:

Maintainer requested deprecation:

Software Package:
ontoCAT

Experiment Data Package:
RnaSeqTutorial
cheung2010



Unresponsive/not-maintained packages:

Software:
GMRP
MBttest
OperaMate
ToPASeq


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] git push to Bioconductor failing

[Hoffman, Gabriel]

Hi,

I am having an issue pushing changes from my git repo to Bioconductor.  I can 
push changes to Github just fine.


Here my push command fails.


> git push upstream

FATAL: W any packages/variancePartition gabrielhoffman DENIED by fallthru

(or you mis-spelled the reponame)

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.

I have the proper upstream location set


> git remote -v

origin https://github.com/GabrielHoffman/variancePartition.git (fetch)

origin https://github.com/GabrielHoffman/variancePartition.git (push)

upstream g...@git.bioconductor.org:packages/variancePartition (fetch)

upstream g...@git.bioconductor.org:packages/variancePartition (push)


But it seems like I don't have write access to this repo.


> ssh -T g...@git.bioconductor.org | grep variancePartition

 R  packages/variancePartition



I have registered my SSH RSA key with Bioconductor, and I have received the 
emails saying it was approved.  But I still do not have write access.


Do you have any suggestions to debug this?


Thanks,

- Gabriel




--

Gabriel Hoffman, Ph.D.



Assistant Professor

Icahn Institute for Genomics and Multiscale Biology

Department of Genetics and Genomic Sciences

Icahn School of Medicine at Mount Sinai



gabriel.hoff...@mssm.edu



1425 Madison Avenue

New York, NY 10029

Icahn Building L3-70B

212-659-1635


http://gabrielhoffman.github.io

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[Bioc-devel] git push to Bioconductor failing

[Hoffman, Gabriel]

n> git push upstream

FATAL: W any packages/variancePartition gabrielhoffman DENIED by fallthru

(or you mis-spelled the reponame)

fatal: Could not read from remote repository.


Please make sure you have the correct access rights

and the repository exists.



> ssh -T g...@git.bioconductor.org | grep variancePartition

 R   packages/variancePartition





> git remote -v

origin https://github.com/GabrielHoffman/variancePartition.git (fetch)

origin https://github.com/GabrielHoffman/variancePartition.git (push)

upstream g...@git.bioconductor.org:packages/variancePartition (fetch)

upstream g...@git.bioconductor.org:packages/variancePartition (push)

[[alternative HTML version deleted]]

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Re: [Bioc-devel] workflow page reorganization

[Shepherd, Lori]

Thanks for this!


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Andrzej Ole� 

Sent: Friday, December 15, 2017 10:27:55 AM
To: Aaron Lun
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] workflow page reorganization

Hi Aaron,

thank you for taking the lead. I've merged your suggested categories with
my preliminary arrangement (which just went online). I've also included an
index at the beginning of the page.

Any refinements are of course welcome, e.g. via PR to
https://github.com/Bioconductor/bioconductor.org

Cheers,
Andrzej


On Fri, Dec 15, 2017 at 2:08 PM, Aaron Lun  wrote:

> My proposed categories reflect my vested interests, but here goes:
>
> - Gene expression:
> - rnaseqGene
> - RNAseq123
> - ExpressionNormalizationWorkflow
> - RnaSeqGeneEdgeRQL
>
> - Epigenomics: (not quite sure what to call this)
> - chipseqDB
> - methylationArrayAnalysis
> - generegulation
>
> - Single cell:
> - simpleSingleCell
> - cytofWorkflow (or in proteomics?)
>
> - Proteomics:
> - proteomics
> - highthroughputassays
> - cytofWorkflow (see above)
>
> - Variant calling:
> - Variant calling
> - Nucleotide tallies
> - eQTL
>
> - Resource querying: (needs a better name)
> - recountWorkflow
> - TCGAWorkflow
>
> - Other:
> - everything else.
>
> I haven't looked at the Basic workflows, which are probably basic enough
> to be lumped together in that existing section.
>
> -A
>
> On 15/12/17 12:33, Shepherd, Lori wrote:
> > Hello all,
> >
> >
> > There has been a request to reorganize the workflow page as workflows
> have grown past basic and advanced.
> >
> >
> > http://bioconductor.org/help/workflows/
> >
> >
> > We wanted to check with the community what your thoughts were for
> categories.
> >
> > Thank you for your suggestions.
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] workflow page reorganization

[Michael Love]

This already looks much improved, thanks Andrzej and Aaron. I think
workflows are where it's at, and this page is probably
underappreciated by Bioconductor users and the outside community.

My wishlist for the workflows page, which may exceed what is available
for the current effort:

1) It should say at the top which version of R/Bioconductor the
workflows are being built on.

2) On the main page, for each workflow:

* A thumbnail (could live in a pre-specified location in the package)
* Author list (autopopulated from DESCRIPTION)
* Version
* Link to the (most current) F1000Research articles for those which
are published (new field in DESCRIPTION?)
* Some kind of CI "buttony" thing, to indicate to users that these are
live documents
* Key Bioc/R packages used in this worfklow (could this also be an
additional DESCRIPTION field?)

3) I think it would be good to encourage the more stubby workflow
descriptions to add more text, and maybe to decrease the very words
ones, so that it's more consistent. Wow, that's pretty obsessive of
me, but I think it would make the page look more professional.

4) Text somewhere with a link to the support site and how to ask for
help on workflows (e.g. vignette(), ?functionName)

5) An advertisement somewhere for submitting a workflow, link to more
detailed doc elsewhere

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Re: [Bioc-devel] workflow page reorganization

[Aaron Lun]

Thanks Andrzej. And yes, I just put in a PR; I hope itemized sublists 
for a particular workflow (i.e., mine) aren't too ambitious.

I'm thinking about whether "Epigenetics" is the right section heading. 
For greatest generality, you could call it "Genome regulation", which 
bundles all genomic binding/accessibility/methylation stuff together.

I was also pondering whether cytof belongs in Proteomics or Single-cell, 
given the equivalent FACS workflow lives in Proteomics and the nature of 
the data are fundamentally different from single cell genomics datasets. 
But I suppose that's none of my business, I'll leave it to Lukas & co.

It would be nice to see an image analysis workflow up there!

-A

On 15/12/17 15:27, Andrzej Oleś wrote:
> Hi Aaron,
> 
> thank you for taking the lead. I've merged your suggested categories 
> with my preliminary arrangement (which just went online). I've also 
> included an index at the beginning of the page.
> 
> Any refinements are of course welcome, e.g. via PR to 
> https://github.com/Bioconductor/bioconductor.org
> 
> Cheers,
> Andrzej
> 
> 
> On Fri, Dec 15, 2017 at 2:08 PM, Aaron Lun  > wrote:
> 
> My proposed categories reflect my vested interests, but here goes:
> 
> - Gene expression:
>      - rnaseqGene
>      - RNAseq123
>      - ExpressionNormalizationWorkflow
>      - RnaSeqGeneEdgeRQL
> 
> - Epigenomics: (not quite sure what to call this)
>      - chipseqDB
>      - methylationArrayAnalysis
>      - generegulation
> 
> - Single cell:
>      - simpleSingleCell
>      - cytofWorkflow (or in proteomics?)
> 
> - Proteomics:
>      - proteomics
>      - highthroughputassays
>      - cytofWorkflow (see above)
> 
> - Variant calling:
>      - Variant calling
>      - Nucleotide tallies
>      - eQTL
> 
> - Resource querying: (needs a better name)
>      - recountWorkflow
>      - TCGAWorkflow
> 
> - Other:
>      - everything else.
> 
> I haven't looked at the Basic workflows, which are probably basic enough
> to be lumped together in that existing section.
> 
> -A
> 
> On 15/12/17 12:33, Shepherd, Lori wrote:
>  > Hello all,
>  >
>  >
>  > There has been a request to reorganize the workflow page as
> workflows have grown past basic and advanced.
>  >
>  >
>  > http://bioconductor.org/help/workflows/
> 
>  >
>  >
>  > We wanted to check with the community what your thoughts were for
> categories.
>  >
>  > Thank you for your suggestions.
>  >
>  >
>  >
>  > Lori Shepherd
>  >
>  > Bioconductor Core Team
>  >
>  > Roswell Park Cancer Institute
>  >
>  > Department of Biostatistics & Bioinformatics
>  >
>  > Elm & Carlton Streets
>  >
>  > Buffalo, New York 14263
>  >
>  >
>  > This email message may contain legally privileged and/or
> confidential information.  If you are not the intended recipient(s),
> or the employee or agent responsible for the delivery of this
> message to the intended recipient(s), you are hereby notified that
> any disclosure, copying, distribution, or use of this email message
> is prohibited.  If you have received this message in error, please
> notify the sender immediately by e-mail and delete this email
> message from your computer. Thank you.
>  >       [[alternative HTML version deleted]]
>  >
>  > ___
>  > Bioc-devel@r-project.org 
> mailing list
>  > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
>  >
> ___
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Re: [Bioc-devel] workflow page reorganization

[Andrzej Oleś]

Hi Aaron,

thank you for taking the lead. I've merged your suggested categories with
my preliminary arrangement (which just went online). I've also included an
index at the beginning of the page.

Any refinements are of course welcome, e.g. via PR to
https://github.com/Bioconductor/bioconductor.org

Cheers,
Andrzej


On Fri, Dec 15, 2017 at 2:08 PM, Aaron Lun  wrote:

> My proposed categories reflect my vested interests, but here goes:
>
> - Gene expression:
> - rnaseqGene
> - RNAseq123
> - ExpressionNormalizationWorkflow
> - RnaSeqGeneEdgeRQL
>
> - Epigenomics: (not quite sure what to call this)
> - chipseqDB
> - methylationArrayAnalysis
> - generegulation
>
> - Single cell:
> - simpleSingleCell
> - cytofWorkflow (or in proteomics?)
>
> - Proteomics:
> - proteomics
> - highthroughputassays
> - cytofWorkflow (see above)
>
> - Variant calling:
> - Variant calling
> - Nucleotide tallies
> - eQTL
>
> - Resource querying: (needs a better name)
> - recountWorkflow
> - TCGAWorkflow
>
> - Other:
> - everything else.
>
> I haven't looked at the Basic workflows, which are probably basic enough
> to be lumped together in that existing section.
>
> -A
>
> On 15/12/17 12:33, Shepherd, Lori wrote:
> > Hello all,
> >
> >
> > There has been a request to reorganize the workflow page as workflows
> have grown past basic and advanced.
> >
> >
> > http://bioconductor.org/help/workflows/
> >
> >
> > We wanted to check with the community what your thoughts were for
> categories.
> >
> > Thank you for your suggestions.
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> ___
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[Bioc-devel] Updated Deprecated Package List for Bioc 3.7

[Shepherd, Lori]

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly.

The current list of deprecated packages is as follows:

Maintainer requested deprecation:

Software Package:
ontoCAT

Experiment Data Package:
RnaSeqTutorial
cheung2010



Unresponsive/not-maintained packages:

Software:
GMRP
MBttest
OperaMate
ToPASeq


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
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Re: [Bioc-devel] workflow page reorganization

[Andrzej Oleś]

Hi Laurent,

thanks, we might consider this in the future. To get us going, for the
moment we will probably just rearrange the website manually.

On the technical note: even though workflows are now fully fledged
packages, two documents linked from https://bioconductor.org/help/workflows
are just static PDFs. As they are around for some time now, I'm not sure
how up-to-date they are.

Cheers,
Andrzej

On Fri, Dec 15, 2017 at 1:56 PM, Laurent Gatto  wrote:

>
> On 15 December 2017 12:33, Shepherd, Lori wrote:
>
> > Hello all,
> >
> >
> > There has been a request to reorganize the workflow page as workflows
> > have grown past basic and advanced.
> >
> > http://bioconductor.org/help/workflows/
> >
> > We wanted to check with the community what your thoughts were for
> > categories.
>
> Could biocViews be used for this?
>
> For example assign workflows biocViews of the packages they use (either
> all biocViews or those that occur several times). biocViews aren't
> perfect, put this would allow automation and would provide consistency
> with the packages categorisation.
>
> Best wishes,
>
> Laurent
>
> > Thank you for your suggestions.
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
> http://lgatto.github.io/
>
> ___
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>

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Re: [Bioc-devel] workflow page reorganization

[Andrzej Oleś]

Hi,

Motivated by discussions with Aaron I've already started to group the
workflows on the page (but this change didn't propagate to the website
yet). Some common topics I was able to identify so far include:

- Beginner's Worklows authored originally by the core team giving a quite
broad overview of the BioC infrastructure
- Annotations
- RNA Sequencing
- Single-cell Workflows
- Genomic Variants
- Domain Specific

The domain-specific workflows currently includes the "advanced" ones which
focus on a particualar topic otherwise not covered by other workflows.

Cheers,
Andrzej

On Fri, Dec 15, 2017 at 1:33 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> Hello all,
>
>
> There has been a request to reorganize the workflow page as workflows have
> grown past basic and advanced.
>
>
> http://bioconductor.org/help/workflows/
>
>
> We wanted to check with the community what your thoughts were for
> categories.
>
> Thank you for your suggestions.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] workflow page reorganization

[Aaron Lun]

My proposed categories reflect my vested interests, but here goes:

- Gene expression:
- rnaseqGene
- RNAseq123
- ExpressionNormalizationWorkflow
- RnaSeqGeneEdgeRQL

- Epigenomics: (not quite sure what to call this)
- chipseqDB
- methylationArrayAnalysis
- generegulation

- Single cell:
- simpleSingleCell
- cytofWorkflow (or in proteomics?)

- Proteomics:
- proteomics
- highthroughputassays
- cytofWorkflow (see above)

- Variant calling:
- Variant calling
- Nucleotide tallies
- eQTL

- Resource querying: (needs a better name)
- recountWorkflow
- TCGAWorkflow

- Other:
- everything else.

I haven't looked at the Basic workflows, which are probably basic enough 
to be lumped together in that existing section.

-A

On 15/12/17 12:33, Shepherd, Lori wrote:
> Hello all,
> 
> 
> There has been a request to reorganize the workflow page as workflows have 
> grown past basic and advanced.
> 
> 
> http://bioconductor.org/help/workflows/
> 
> 
> We wanted to check with the community what your thoughts were for categories.
> 
> Thank you for your suggestions.
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Cancer Institute
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
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Re: [Bioc-devel] workflow page reorganization

[Laurent Gatto]

On 15 December 2017 12:33, Shepherd, Lori wrote:

> Hello all,
>
>
> There has been a request to reorganize the workflow page as workflows
> have grown past basic and advanced.
>
> http://bioconductor.org/help/workflows/
>
> We wanted to check with the community what your thoughts were for
> categories.

Could biocViews be used for this?

For example assign workflows biocViews of the packages they use (either
all biocViews or those that occur several times). biocViews aren't
perfect, put this would allow automation and would provide consistency
with the packages categorisation.

Best wishes,

Laurent

> Thank you for your suggestions.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited.  If you have 
> received this message in error, please notify the sender immediately by 
> e-mail and delete this email message from your computer. Thank you.
>   [[alternative HTML version deleted]]
>
> ___
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-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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[Bioc-devel] workflow page reorganization

[Shepherd, Lori]

Hello all,


There has been a request to reorganize the workflow page as workflows have 
grown past basic and advanced.


http://bioconductor.org/help/workflows/


We wanted to check with the community what your thoughts were for categories.

Thank you for your suggestions.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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