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GDC CNA files have ensembl transcript ids that are converted to Hugo symbols via Genome Nexus. However, some of the transcript ids are for GRCh38, which is not supported by GN. For these, we need to d…
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It is often useful to annotate orthologous genes to leverage algorithms designed for human/mouse data.
Let's assume we have an anndata object with mouse gene ids in `var_names`. I would like to ha…
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Thanks for your great work! But not all genes have a corresponding ENSG format gene ID, how to deal with it?QAQ
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When working with single-cell datasets from different sources, a common task is to harmonized gene identifiers.
Let's assume, we have an anndata object with gene symbols as `obs_names`:
```pyth…
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Hi @cschlaffner :
Can you explain in details why we can not do the mapping to taxonomies like _Yeast_ or _E.coli_. This issue can be used to trigger the discussion with **ENSEMBL** and explain the…
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> tr2g2
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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…
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Hi,
I am trying to use pyensembl with the GTF for Gencode v19 as I find the pyensembl interface easy to work with, but I need a more highly curated set of transcripts than the ensembl data.
I am usi…
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Hi,
I was following the workflow to create the 'standard' reference library, but instead starting from an updated gencode reference GTF (human v40) to define initial 3'UTR regions. I followed the s…
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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…