[Bioc-devel] Package submission deadline Bioconductor 3.18

[Heery Richard]

Hello,

I am wondering what is the deadline for new package submissions for 
Bioconductor 3.18? I see a release schedule for 3.17 
(https://bioconductor.org/developers/release-schedule/), but nothing similar 
for 3.18 yet.

Best wishes,

Richard Heery
[5x1000]

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Re: [Bioc-devel] Bioconductor data packages containing very large files

[Heery Richard]

Thank you Lori.

I was wondering if there is someone I could  ask if what I am working on could 
be of interest and suitable for Bioconductor before investing more time 
developing it and uploading the data? What I have is a HDF5 file constructed 
using the Bioconductor methrix package for all of the methylation data for TCGA 
downloaded from GDC. It allows rapid querying of methylation data for regions 
of interest (e.g. enhancers or promoters) provided as a GRanges object across 
the ~10,000 samples in TCGA, completing a pan-cancer analysis in minutes . 
Otherwise, downloading and querying data for regions of interest in several 
cancer types could take several days or longer.

There are already packages for downloading TCGA data on Bioconductor, but what 
I think is novel here is the speed and ease with which methylation data can be 
retrieved for a large number of samples.

Please let me know if this is something that could be useful for Bioconductor.

Best wishes,

Richard

From: Kern, Lori 
Sent: Wednesday, January 4, 2023 3:22 PM
To: Heery Richard ; bioc-devel@r-project.org 

Subject: Re: Bioconductor data packages containing very large files

A package cannot be that large directly.  Please see information on creating an 
ExperimentHub package to provide the data for use in the package:

 
https://bioconductor.org/packages/release/bioc/vignettes/HubPub/inst/doc/CreateAHubPackage.html<https://urlsand.esvalabs.com/?u=https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fvignettes%2FHubPub%2Finst%2Fdoc%2FCreateAHubPackage.html&e=8c00e339&h=ddd80e7a&f=y&p=n>

Cheers,




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Heery Richard 

Sent: Wednesday, January 4, 2023 9:07 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioconductor data packages containing very large files

Hi Bioconductor,

I have made a database that is 27 GB that I would like to share as part of a 
Bioconductor package and I was just wondering if it is possible to submit very 
large files like this to Bioconductor or if there may be any alternative ways 
of sharing the file as part of a package?

Best wishes,

Richard Heery

IEO, Milan, Italy
[5x1000]<http://secure-web.cisco.com/1AxunlkMfMiOLWUzSr4U79PCQR-m5gepMk3mVQ7uLXKMCAeTNzkyygmALFERcsVxhVSX7zkAFcllkjIZnZKxUh80DdGusfFIL4XGxaAJXK-2sG43sKOXakdJVd8cDp7HQArb01uoPUuJlVHlAaVSxuLW-ZABWxKwog7MokYLudEkL7-ib-hPb7R2WajUM6LmVWyXT51DcWzhFVIHJ4LNCbfelON_k_SA2ybm5NUGX7cKNLFpUIW2cmp2rhue-arnJ30_cFqdxWgDzajh8Nt87OFWo51fE4_OyTrtBO-CG555adYVMuYutSliHgvl1_BGs/http%3A%2F%2Fwww.ieo.it%2Fit%2FSCIENCE-IN-SOCIETY%2FLe-nostre-iniziative%2F5-per-mille%2F><https://urlsand.esvalabs.com/?u=http%3A%2F%2Fsecure-web.cisco.com%2F1AxunlkMfMiOLWUzSr4U79PCQR-m5gepMk3mVQ7uLXKMCAeTNzkyygmALFERcsVxhVSX7zkAFcllkjIZnZKxUh80DdGusfFIL4XGxaAJXK-2sG43sKOXakdJVd8cDp7HQArb01uoPUuJlVHlAaVSxuLW-ZABWxKwog7MokYLudEkL7-ib-hPb7R2WajUM6LmVWyXT51DcWzhFVIHJ4LNCbfelON_k_SA2ybm5NUGX7cKNLFpUIW2cmp2rhue-arnJ30_cFqdxWgDzajh8Nt87OFWo51fE4_OyTrtBO-CG555adYVMuYutSliHgvl1_BGs%2Fhttp%253A%252F%252Fwww.ieo.it%252Fit%252FSCIENCE-IN-SOCIETY%252FLe-nostre-iniziative%252F5-per-mille%252F%26gt%3B&e=8c00e339&h=13a49eac&f=y&p=n>

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[Bioc-devel] Bioconductor data packages containing very large files

[Heery Richard]

Hi Bioconductor,

I have made a database that is 27 GB that I would like to share as part of a 
Bioconductor package and I was just wondering if it is possible to submit very 
large files like this to Bioconductor or if there may be any alternative ways 
of sharing the file as part of a package?

Best wishes,

Richard Heery

IEO, Milan, Italy
[5x1000]

[[alternative HTML version deleted]]

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