update: this approach bases on Martin's suggestion and I think is ideal for
EnsDb or any Ensembl based annotation packages. It's not required to install an
explicit genome package, but load (and eventually cache) dynamically the
correct genomic sequence from Ensembl via AnnotationHub. That way c
On 06/10/2015 01:11 AM, Rainer Johannes wrote:
Dear Martin,
the AnnotationHub approach looks awesome! However, somehow it does not work for
me, I always get an error:
library(AnnotationHub)
library(Rsamtools)
library(GenomicFeatures)
ah <- AnnotationHub()
## somehow I don't see DNA sequences f
update:
seems something is strange with the index... when I load the ensembl-77 DNA for
mouse I get two files, the fasta file and the index and I can extract the
sequences, while in the example below I just got the fasta file
On 10 Jun 2015, at 10:11, Rainer Johannes
mailto:johannes.rai...@eur
dear Ludwig,
On 10 Jun 2015, at 10:29, Ludwig Geistlinger
mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
Dear Johannes,
one follow-up question/comment on the EnsDb packages:
The reason they escaped my notice (and thus potentially will also others)
is that I expected such packages to be nam
Dear Johannes,
one follow-up question/comment on the EnsDb packages:
The reason they escaped my notice (and thus potentially will also others)
is that I expected such packages to be named "^TxDb...".
What actually argues against sticking to existing Bioc vocabulary and
naming eg EnsDb.Hsapiens.v
Dear Martin,
the AnnotationHub approach looks awesome! However, somehow it does not work for
me, I always get an error:
library(AnnotationHub)
library(Rsamtools)
library(GenomicFeatures)
ah <- AnnotationHub()
## somehow I don't see DNA sequences for release-80... thus using 75
query(ah, c("Taki
On 06/08/2015 11:43 PM, Rainer Johannes wrote:
dear Robert and Ludwig,
the EnsDb packages provide all the gene/transcript etc annotations for all
genes defined in the Ensembl database (for a given species and Ensembl
release). Except the column/attribute "entrezid" that is stored in the
internal
dear Ludwig,
On 09 Jun 2015, at 10:46, Ludwig Geistlinger
mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
Dear Johannes,
Thx for providing the great EnsDb packages!
One question:
As of now, I am able to choose between TxDb and EnsDb for genomic
coordinates of genomic features such as genes
Dear Johannes,
Thx for providing the great EnsDb packages!
One question:
As of now, I am able to choose between TxDb and EnsDb for genomic
coordinates of genomic features such as genes, transcripts, and exons.
For the sequences themselves I need the corresponding BSgenome package.
While it is e
dear Robert and Ludwig,
the EnsDb packages provide all the gene/transcript etc annotations for all
genes defined in the Ensembl database (for a given species and Ensembl
release). Except the column/attribute "entrezid" that is stored in the internal
database there is however no link to NCBI or
Ludwig,
If you do this search on the UCSC genome browser (which this annotation
package is built from), you will see that the longest variant is what is
shown
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg38&position=brca1&hgt.positionInput=brca1&hgt.suggestTrack=knownGene&S
Dear Bioc annotation team,
Querying TxDb.Hsapiens.UCSC.hg38.knownGene for gene coordinates, e.g. for
BRCA1; ENSG0012048; entrez:672
via
> genes(TxDb.Hsapiens.UCSC.hg38.knownGene, vals=list(gene_id="672"))
gives me:
GRanges object with 1 range and 1 metadata column:
seqnames
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