Hi --
Bioconductor has sometimes participated in Google Summer of Code
(https://developers.google.com/open-source/gsoc/timeline?hl=en ,
https://developers.google.com/open-source/gsoc/faq#how_does_a_mentoring_organization_apply).
If there is interest in the community to sponsor participation (f
On 01/09/2016 08:42 AM, Michael Lawrence wrote:
I can understand the desire to avoid defining and enforcing our own
standards on third-party data: it's error-prone, potentially
confusing, etc. But the same is even more true of expecting the user
to perform the mapping via some adhoc approach.
It
Also things like organismdbi don't seem to exist for organisms other than
human, mouse, rat. So if you want to use that infrastructure for fly or worms,
you're SOL at the moment.
This is a highly topical discussion since many/most microarray probes can be
profitably (in terms of knowledge, no
I can understand the desire to avoid defining and enforcing our own
standards on third-party data: it's error-prone, potentially
confusing, etc. But the same is even more true of expecting the user
to perform the mapping via some adhoc approach.
It's unfortunate that Ensembl does not follow the co
We switched to TwoBitFile with a recent ensembl release, thinking that it had
better performance and other characteristics compared to the previous FaFile.
The 'recipe' used to create the FaFiles did not explicitly trim the label; that
appears to be something done by Rsamtools::indexFa and hence
Yes, using BSGenome would help in this case.
In the long run I think it might be important to have this fixed, not
necessarily for human, but for other species/genome builds for which there
might not be an BSGenome package available; through AnnotationHub all GTF files
and fasta files would be
