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
# $rdataclass: TwoBitFile
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH65579"]]'
title
AH65579 | Caenorhabditis_elegans.WBcel235.cdna.all.2bit
AH65580 | Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.2bit
AH65581 | Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.2bit
AH65582 | Caenorhabditis_elegans.WBcel235.ncrna.2bit
Also to get the path of the AnnotationHub downloaded resorurce please use the
format
cache(ah["AH50789"])
instead of
ah[["AH50789"]]$path
Cheers,
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-boun...@r-project.org> on behalf of Julien
Wollbrett <julien.wollbr...@unil.ch>
Sent: Tuesday, January 22, 2019 8:57:23 AM
To: bioc-devel@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/>
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,
Julien
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