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I keep getting this warning even though the readme file is in the same directory as the tabix formatted data file.
WARNING: Failed to instantiate plugin dbNSFP: ERROR: Could not retrieve dbNSFP ver…
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Hi Mike @grimbough
We're seeing this SSL error from the `listMarts` function in `GenomicFeatures`:
https://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicFeatures/nebbiolo1-checksrc.html
…
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#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify.
(ru…
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Hello,
I try to run VEP using Singularity on Linux system. I downloaded cache file, extracted it in scratch folder, and tried to use it with --dir_cache option, but with error (message below). How s…
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We see more and more people express interests in using the T2T CHM13 v1.1 as the reference, or at least giving that a try.
So I'm wondering if it makes sense to add it to the genome list, though it…
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Sure!
Fetching transcripts, getting locations on X and Y:
https://www35.lamp.le.ac.uk/VariantValidator/tools/gene2transcripts/SHOX?content-type=application%2Fjson
LOVD deleting a base inside this…
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For instance SKI gene: https://grch37.rest.ensembl.org/xrefs/symbol/homo_sapiens/SKI?external_db=HGNC
At the moment only the second Ensembl ID is captured, but this might lead to less matching resu…
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We have had several requests to provide exon numbering. I have always avoided this because it is a total mine field
Although this is a seemingly trivial thing to do but it is actually hugely compli…
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**Is your feature request related to a problem? Please describe.**
Not related to a problem but will be an upgrade of the select_transcripts feature
**Describe the solution you'd like**
1. We now…
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When creating a new Gene-Disease record, the first step in the Gene Curation interface is to add the approved HGNC gene symbol (field:Enter HGNC gene symbol *). However genes are commonly known by oth…