[Bioc-devel] Best practices to load data for vignette/tests

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Jan 24 14:44:11 CET 2019

The transcriptome datasets switched to 2Bit files.  We do provide the updated TwoBitFiles in the annotatiuonhub  (again we have not yet added 95 but do have 94).

> query(hub, c("ensembl", "elegans", "release-94", "2bit"))
AnnotationHub with 4 records
# snapshotDate(): 2019-01-14
# $dataprovider: Ensembl
# $species: Caenorhabditis elegans
# $rdataclass: TwoBitFile
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH65579"]]'

  AH65579 | Caenorhabditis_elegans.WBcel235.cdna.all.2bit
  AH65580 | Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.2bit
  AH65581 | Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.2bit
  AH65582 | Caenorhabditis_elegans.WBcel235.ncrna.2bit

Also to get the path of the AnnotationHub downloaded resorurce please use the format


instead of



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Julien Wollbrett <julien.wollbrett using unil.ch>
Sent: Tuesday, January 22, 2019 8:57:23 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Best practices to load data for vignette/tests

Hi everyone,

I am currently working on a R package called BgeeCall allowing to
automatically generate present/absent expression calls from any RNA-Seq
fastq files as long as the species is present in Bgee (https://bgee.org/)
Welcome to Bgee: a dataBase for Gene Expression Evolution<https://bgee.org/>
Gene expression data. Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data).

The package is almost ready and I am currently writing the vignette and
some tests.

This package can be seen as a workflow taking as input one transcriptome
and at least one fastq file.

My question is how can I import these 2 files to run the vignette/tests?
They are too big to be part of my package.
Can I directly download them from SRA and ensembl (or from my own
server)? Do I need to create a dataset that will be loaded by my package
for this kind of raw and publicly available data?
Do you know if I could reuse some already existing dataset? I am
interested to any best practices infomation.
Thank you for your answers.

Best Regards,


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