Hi Hamada,
Bioconductor has two branches - release and development. ExperimentHub
has been added to the devel branch of Bioconductor recently -and it
will thus work only with the devel version of R until it is added to the
release branch ( April 15th, 2016)
The release schedule can be found he
ostrings", "BSgenome", "VariantAnnotation").
Please let me know if the problem continues after re-installing these packages.
I have bumped the versions of each of these packages, so that biocLite() after
tomorrow-ish should force these to be re-installed.
Usually 'm
Hi everyone,
I am trying to get a FaFile from AnnotationHub - It fails with the
following error
library(AnnotationHub)
ah =AnnotationHub()
ah = query(ah , c("Homo sapiens", "org", "GRCH37", "FASTA","75"))
hg37_rna = ah[["AH10879"]]
> hg37_rna = ah[["AH10879"]]
require(“Rsamtools”)
Error: fail
On a slightly similar note,
I also feel that we should have a map available ( possibly in the
vignette of GenomeInfoDb, under seqlevelsStyle)
something like this
(http://www.gencodegenes.org/releases/reference_releases.html)
which tells people the corresponding versions between UCSC/NCBI/GENCO
Hi Tom,
1) Duplicate names in fasta file
You were right! Fixed.. Thanks.
2) You're right ! The seqlevels in the fasta file have an additional
column with the gene description (as shown below)
> head(seqlevels(fastaCDS))
[1] "gi|584277002|ref|NM_001289933.1| Homo sapiens ZO-2 associated
sp
