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I would like goa_ref to be the default GAF for human, but we need to ensure things are in sync. Background: https://sourceforge.net/p/geneontology/annotation-issues/1306/
Unfortunately the SP/TR IDs …
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I tried the following to filter based on entrez gene id
```
server = Server(host='http://www.ensembl.org')
dataset = (server.marts['ENSEMBL_MART_ENSEMBL']
.datasets['hsapiens_…
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### --> No gene can be mapped....
Hi,
I have tried to look for solutions for this in SO, biostars, bioconductor, your html manual, the PDF vignette, and your GitHub issues... nothing has worked,…
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**User story**
Some users might be interested in Ensembl IDs while others might want to use gene symbols. in v1.1.20 we added the `geneAlias` support for using one of the two (but not both)
**Pr…
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### Context
We received an email.
### Problem or idea
A number of the histone genes have undergone revision and deconvolution in ENSEMBL recently. For example:
http://www.ensembl.org/Homo_sa…
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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
4 months ago
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Hello,
when using Pizzly 0.37.3 (SeqAn 2.2.0) and Kallisto 0.43.1 with Ensembl 81 and one gets this error message from Pizzly:
```
Error, could not find any transcript sequences check that the i…
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Hello,
I am using CollecTRI to study mouse genome, when I run in R `net
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**Describe the bug**
The Metric `cell_cycle_conservation` fails with datasets from the Cell x Gene Census:
```
ValueError: cell cycle genes not in adata
organism: human
varnames: ['ENSG00000105…
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As a bioinformatics analyst I want to generate a BED file from a gene panel for genomic test analysis so that I can use it as an input to an NGS pipeline tool.
- [ ] Get gene panel from panelapp, ref…