-
It seems that short_long does not support files without gene lines. I think the gene_ids should could taken from the transcript lines or even the exon line since it is very common to have no gene line…
-
The batch query portal is a popular feature in our website. It has been long realised that the Batch Query portal requires improvement of data display.
We assume an allele-based display of the data (…
-
Currently, each gene in cellxgene has only one name associated with it (the Index of `adata.var`). However, the other fields in `adata.var` can be used to hold alternative gene IDs. For example, if th…
-
### 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 …
-
We're currently only extracting gene acronyms (whether canonical or noncanonical), ensembl IDs and RefSeq IDs. In sentences such as the following:
`SDF-1 and CXC receptor 4 ( CXCR4 ) expression in rh…
-
I use pyensembl for gene id/name mapping but lately I noticed that some ensembl gene ids (e.g. ENSG00000285395) are missing in `pyensembl.EnsemblRelease(97).genes()`.
That's I think because pyense…
-
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
-
Could add a mapping of Ensembl transcript IDs to NCBI RefSeq ID(s?).
In the Perl API:
```
my @dbentries = @{ $transcript->get_all_DBEntries() };
```
On the db entry: `dbname()` to get the name …
-
Is there a way to filter genes returned to only return ENSG's of HGNC genes in Ensembl? Maybe this should be added as a function.
-
I am performing DIA-NN from FASTA digest library for Arabidopsis thaliana. I got FASTA file from [**_plants.ensembl_**](https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-58/fasta/arabidopsis_tha…