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that looks great, thanks Hervé for addressing this quickly.
robert.
On 1/11/16 11:18 PM, Hervé Pagès wrote:
With GenomicFeatures 1.23.16:
> txdb <- makeTxDbFromUCSC("hg38", "knownGene")
Download the knownGene table ... OK
Download the knownToLocusLink table ... OK
Extract the 'transcripts'
Just as an info… EnsDb objects/packages (from ensembldb package) provide
similar functionality than the TxDb, are tailored to Ensembl annotations and
can be build from the GTF files from Ensembl (which can be fetched via
AnnotationHub; it’s all described in the ensembldb vignette).
cheers, jo
Hi Vince, Robert,
On 01/11/2016 07:07 AM, Vincent Carey wrote:
On Mon, Jan 11, 2016 at 9:29 AM, Robert Castelo
wrote:
hi,
if i'm interpreting this correctly, the news archive of the UCSC Genome
Browser accessible here:
Hi Robert and others,
I looked at this and the new situation doesn't seem as disruptive as
it sounds. The bulk of the data for both tracks (i.e. the "UCSC Genes"
track for hg19 and the "GENCODE v22" track for hg38) is stored in the
knownGene table.
The hg19.knownGene table is described here:
Tim, you always crack me up! :) I totally agree, and it would probably be
good to also have the tools enabled to download directly from Ensembl, NCBI,
cloud-annotation source, etc. and build/update the AnnDbBimap objects. This
way the annotation sources can maintain the data and us the scripts,
The Bioconductor team has an opening available for a Senior Progammer /
Analyst, see
https://www.roswellpark.org/careers/administrative/senior-programmeranalyst-4301
for details. Bioconductor is an exciting and reward work environment.
Please contact me (martin.morgan at roswellpark.org)
hi,
if i'm interpreting this correctly, the news archive of the UCSC Genome
Browser accessible here:
http://genome.ucsc.edu/goldenPath/newsarch.html
announced on June 29th, 2015, that they are discontinuing the generation
of UCSC Known Genes annotations for human, and provide the Gencode
On Mon, Jan 11, 2016 at 9:29 AM, Robert Castelo
wrote:
> hi,
>
> if i'm interpreting this correctly, the news archive of the UCSC Genome
> Browser accessible here:
>
> http://genome.ucsc.edu/goldenPath/newsarch.html
>
> announced on June 29th, 2015, that they are
hi,
On 01/11/2016 04:07 PM, Vincent Carey wrote:
[...]
Is it true that there is an asymmetry between Entrez gene ID and Ensembl
gene ID for querying org.Hs.eg.db (I tend to prefer Homo.sapiens
as a symbol mapping resource)? Both ENTREZID and ENSEMBL are listed as
keytypes. My question is
I think these are all good observations and we may benefit from a wider
discussion on the support site?
the abandonment of knownGene seems to have clear implications for changing
our most visible txdb
examples. what should we change to? can we make a more future-proof
design for these
ENSEMBL
knownGene was always a disaster. For extra amusement/horror, be sure to
check out the sad saga of the TCGA GAF and its disconnection from
knownGenes as well as reality. Three cheers for rendering transcript-level
estimates useless (and no this was not Katie's fault)
Rainer and many
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