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There is a difference in the result between refseq and ensembl and I'm not too sure why.
Basically when the genome build is GRCh38 and transcript_set is 'refseq', the variant `11-5248232-T-A` it s…
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### Description of the bug
do I need to use my local version of R?
### Command used and terminal output
```console
Hi guys, I have tested hicar 1.0.0 "nextflow run nf-core/hicar -r 1.0.0 -profile t…
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This may not be needed based on the recent PR but when running, a timeout occurs and setting options(timeout) does not work
```
processing gene2pubmed
processing gene_info: chromosomes
processi…
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The goal is to use entrez gene_ids rather than hgnc symbols to link genes and transcripts, including dropping the hgnc column from the transcript table.
Phase 1:
* Update gene table schema and loa…
reece updated
5 months ago
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There are some URI's (issue found with geneIDs)that are expanded massively and when used in another call (target info for example) give a 500 error
Examples:
http://identifiers.org/ncbigene/5327
h…
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hi @lachmann12. I really appreciate this resource , it is truly great help. But apparently I noticed [this]( https://github.com/MaayanLab/archs4/issues/38#issue-2106403213) too and as you may s…
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Hi,
Thanks for your tools. When I used transId to transform gene ids, I found that this tool sometimes works fine, but sometimes it gives an error：
```
ec
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### Description of feature
It would be nice to have an example where we directly connect to the ensembl mysql servers to run a query. Especially for the biomart version, much more information should …
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ENSP00000328848 has 852 amino acids:
http://annotation.genomenexus.org/ensembl/transcript?proteinId=ENSP00000328848
But Ensembl has 995:
http://useast.ensembl.org/Homo_sapiens/Transcript/ProteinS…
jjgao updated
6 years ago
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Hi Tian
I enumerated and annotated an ensemble gene ID of interest, however, when I attempt to save the query a message pops up indicating "writing CSV file". However, this window never closes and t…