User: kayla.interdonato

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40
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New User
Location:
United States
Last seen:
20 hours ago
Joined:
1 year, 4 months ago
Email:
k************@roswellpark.org

Bioconductor Core Team Member.

I work as a Bioconductor Core Team Member out of Roswell Park Comprehensive Cancer Center in Buffalo, NY.  I help maintain the Single Package Builder for new submissions, the main Bioconductor website, and this support site. I also provide help along with all members of the team to offer support and maintenance of core package and core structures, but I am responsible for the standard annotation packages.

Posts by kayla.interdonato

<prev • 7 results • page 1 of 1 • next >
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Answer: A: HLA genes missing from TxDb.Hsapiens.UCSC.hg38.knownGene
... Try setting the `single.strand.genes.only` argument for `genes()` to `FALSE`, then you will be able to access these genes. ``` > library(TxDb.Hsapiens.UCSC.hg38.knownGene) > regions <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene, single.strand.genes.only = FALSE) > names(regions)[1:5] [1] ...
written 3 days ago by kayla.interdonato40
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News: Bioconductor 3.10 db0s are available
... The newest db0 packages for the upcoming Bioconductor 3.10 release are up and should propagate within a day or so. The deadline for submitting contributed annotations will be **Wednesday October 23rd**. The new db0 packages are: anopheles.db0_3.10.0.tar.gz arabidopsis.db0_3.10.0.tar.gz bovine.db0_ ...
annotation db0 news release deadline written 3 months ago by kayla.interdonato40
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Comment: C: kegg.gsets: unknown species
... I've never used gage and I don't want to mess up your script that you already have working, but another possibility would be to use the package [KEGGREST](https://bioconductor.org/packages/release/bioc/html/KEGGREST.html). ``` > library(KEGGREST) > head(keggList("spis")) ...
written 3 months ago by kayla.interdonato40
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Comment: C: AnnotationDbi 1.46.0 not available in archive of Bioconductor 3.9 release?
... This was due to an issue with the build code. This tarball had to be created by hand, hence the minor differences such as time stamps. Unfortunately, we are not able to restore the original source tarball but the code is now more robust to decrease the occurrence of this issue in the future. ...
written 4 months ago by kayla.interdonato40
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Comment: C: AnnotationDbi 1.46.0 not available in archive of Bioconductor 3.9 release?
... The archive is now available and can be found [here][1] or at the end of the landing [page][2] for AnnotationDbi. [1]: http://bioconductor.org/packages/3.9/bioc/src/contrib/Archive/ [2]: https://bioconductor.org/packages/3.9/bioc/html/AnnotationDbi.html ...
written 4 months ago by kayla.interdonato40
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Answer: A: AnnotationDbi 1.46.0 not available in archive of Bioconductor 3.9 release?
... We are looking a bit deeper into the archive issue. As far as the outdated NEWS file, you can take a look at the commits made to AnnotationDbi on the GitHub [repo][1]. [1]: https://github.com/Bioconductor/AnnotationDbi/commits/RELEASE_3_9 ...
written 4 months ago by kayla.interdonato40
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Answer: A: BioC2018 Workshop book not linked from Bioconductor.org?
... Thank you for pointing this out. The material is now added to the [Courses and Conferences][1] on the Bioconductor website. [1]: https://www.bioconductor.org/help/course-materials/ "Courses and Conferences" ...
written 9 months ago by kayla.interdonato40

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