[Bioc-devel] Dependency files question

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Mar 4 13:18:19 CET 2020

We would probably recommended having an associated data package that utilizes ExperimentHub.  Please see

Please let me know if you have any follow up questions.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Alexandru Voda <alexandru.voda using seh.ox.ac.uk>
Sent: Monday, March 2, 2020 6:51 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Dependency files question


Hope this finds you well!

I was told to contact this mailing list about preparing/changing a package for Bioconductor submission.

My question is: How should I store large dependency files - 6GB large (e.g. 1000 genomes reference LD data) - for the package on Bioconductor?

My package wraps multiple methods of cell-typing GWAS summary statistics. The problem is that the methods wrapped by my package require dependency files for analyses to run, and those dependency files are very large. In my github package, I simply made a function that downloads and formats all of the data in the package's system path, in the data folder: paste0(system.file(package="GWASCellTyper"), "/data/")

Link to the package in its current state: https://bitbucket.org/alexandru_ioan_voda/cell_typing_package/src/master/

With best wishes,

Alexandru Ioan Voda

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