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News: Ensembl 79 release is out!
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gravatar for amonida
2.7 years ago by
amonida10
United Kingdom
amonida10 wrote:

Ensembl e79 is now out with the following Biomart changes:

* Ensembl Genes 79
    Split up the id list and id list limit filters to separate external references from probes filters

        Renamed "Limit to genes..." to "Limit to genes (external references)..." and "Limit to genes (microarray probes/probesets)..."

        Renamed "ID list limit" to "Input external references ID list" and "Input microarray probes/probesets ID list"
    Separated the Variation page into Variation (Germline) and Variation (Somatic)
        Renamed "chromosome_location" internal name to "chromosome_start" and added a new attribute called "chromosome_end" in the Variation (Germline) page
        Renamed "somatic_chromosome_location" internal name to "somatic_chromosome_start" and added a new attribute called "somatic_chromosome_end" in the Variation (Somatic) page
        Renamed "Chromosome Location (bp)" attribute to "Chromosome position start (bp)" in both Variation (Germline) and Variation (Somatic) pages
    Fruitfly (Drosophila melanogaster) assembly update from BDGP5 to BDGP6 and geneset update
    Human assembly update from GRCh38 to GRCh38.p2
    Ensembl Variation 79
    Removed the "_20137" from all the variation_citation attributes internal names
    Removed all the "_20126" from all the regulatory feature attributes internal names and prefixed all the internal names with "reg_"
    Removed all the "_20125"  from all the motif feature attributes internal names and prefixed all the internal names with "motif_"
    Fruitfly (Drosophila melanogaster) assembly update from BDGP5 to BDGP6 and geneset update
    Human assembly update from GRCh38 to GRCh38.p2
* Ensembl Regulation 79
    Brand new Regulation mart, faster, easier to use and packed with new features. Feature set has been split up into 6 sections.
    Added Band Start and End filter
    Added Marker Start and End filter
    Added Encode region filter
    Added SO name and accessions for the 6 Regulation sections
    Added EFO Term accessions for Regulatory evidence, Regulatory features and Regulatory segments.
    Added  "Has evidence" data to the Regulatory features section
    Added Strand and "Evidence" to the miRNA Target Regions section.
* Vega 59
    Renamed "ID list limit" to "Input external references ID list"
    Human assembly update from GRCh38 to GRCh38.p2

For the full details of the release please refer to http://www.ensembl.org/info/website/news.html.

Best regards,
Amonida

ADD COMMENTlink modified 2.7 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.7 years ago by amonida10

Hi Amonida,

Thanks for announcing new Ensembl releases here. In the future could you please select Post Type -> "News event" when you fill the Post Form so the announcement shows up as a News and not as a Question. Thanks in advance!

Best,

H.

ADD REPLYlink written 2.7 years ago by Hervé Pagès ♦♦ 13k
Hi Herve, Sure, I'll keep that in mind for next time. Cheers, Amonida On 13/03/2015 16:45, Hervé Pagès [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User Hervé Pagès <https: support.bioconductor.org="" u="" 1542=""/> wrote > Comment: Ensembl 79 release is out! > <https: support.bioconductor.org="" p="" 65636="" #65643="">: > > Hi Amonida, > > Thanks for announcing new Ensembl releases here. In the future could you > please select Post Type -> "News event" when you fill the Post Form so > the announcement shows up as a News and not as a Question. Thanks in > advance! > > Best, > > H. > > ------------------------------------------------------------------------ > > You may reply via email or visit > C: Ensembl 79 release is out! >
ADD REPLYlink written 2.7 years ago by amonida10

The post author or a moderator (you or I) can change the post type after the fact. I went ahead and did it for this post.

ADD REPLYlink written 2.7 years ago by Dan Tenenbaum ♦♦ 8.2k

Perfect! Thanks Dan.

ADD REPLYlink written 2.7 years ago by Hervé Pagès ♦♦ 13k
Thanks for that Dan! Cheers, Amonida On 14/03/2015 00:53, Dan Tenenbaum [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User Dan Tenenbaum <https: support.bioconductor.org="" u="" 4256=""/> wrote > Comment: Ensembl 79 release is out! > <https: support.bioconductor.org="" p="" 65636="" #65670="">: > > The post author or a moderator (you or I) can change the post type after > the fact. I went ahead and did it for this post. > > ------------------------------------------------------------------------ > > You may reply via email or visit > C: Ensembl 79 release is out! >
ADD REPLYlink written 2.7 years ago by amonida10
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