Re: [Bioc-devel] workflow page reorganization

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

Re: [Bioc-devel] workflow page reorganization

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 >

Re: [Bioc-devel] workflow page reorganization

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

[Bioc-devel] workflow page reorganization

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

Re: [Bioc-devel] workflow page reorganization

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 -

[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:

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

Re: [Bioc-devel] workflow page reorganization

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

Re: [Bioc-devel] workflow page reorganization

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

Re: [Bioc-devel] workflow page reorganization

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�

[Bioc-devel] git push to Bioconductor failing

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

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

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,

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

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.

[Bioc-devel] git push to Bioconductor failing

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

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

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

Re: [Bioc-devel] 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: >

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

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