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Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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'

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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:

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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:

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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,

[Bioc-devel] R / Bioconductor job opportunity: Senior Programmer / Analyst

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)

[Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

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