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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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Hello,
Depending on many factors, number of genes matching between input gene matrix and reference genesets can vary and depending on the tool, it can sometimes add variation in the output. It woul…
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Casual user may want to pass in an entire SCE but just the rho matrix corresponding to their marker genes. In theory we should be able to detect this and appropriatley subset the SCE by matching the `…
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Hi, I'd like to use your library but I'm getting endless errors for retired ENSG ids. How should I proceed when I get errors like this one?
ensembl.gene_name_of_gene_id("ENSG00000129277")
"""
Value…
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Hello,
I am using the Pascal package, which contains an annotation file with UCSC known genes. However, I would like to use it with ENSG identifiers.
In the settings.txt file included in the package…
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When trying to refer to ensembl transcripts we cannot find by version in the 20210129 data release.
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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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Hello,
I just want to report an incompatibility with the latest version of data.table ([recently published in CRAN](https://cran.r-project.org/web/packages/data.table/index.html)).
Using data.table=…
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Hi,
I would like to use mygene with R to convert entrezid from one species (a non model species, taxid= 56716) to zebrafish (basically I need the homologous genes), but from the vignette is not clear…
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Roadmap:
- We will limit ourselves to the annotation providers gencode and ensembl for now.
- We will try to stay ID centric where possible, ie route mappings through IDs.
Basic improvements to c…