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@DongqiangZeng0808
https://github.com/IOBR/IOBR/blob/master/R/count2tpm.R#L55
In the `count2tpm` function, the author seems to simply use `end_position - start_position` (in Line 55) to calculate…
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- [ ] edit `run-the-plan` script to load `library(config)` and remove `config::` statements
- [ ] lint code
- [ ] `count_df` is a misleading argument name, it is a matrix not a df
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Hello,
I'm trying to use bioMart to retrieve the gene names from Apis mellifera from Ensemble. I'm trying to analyze the data generated by Kallisto using Sleuth.
I encounter the error posted in …
nmorf updated
2 years ago
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Hi team,
Thank you for the nice explanation about database building. I want to create a database for zebrafish using "create_cistarget_motif_databases.py". I am struggling to get a zebrafish genom…
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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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Thanks for your work！
However， in 02_EC19001-SC2100428-Tissue-global.ipynb，it shows "done with scanpy-recipes with jupyterlab_1.3.1.sif".
I can't find it in the page. Could you offer it ? Thanks a l…
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We currently only have/use ortholog mappings provided by the [Alliance of Genomes](https://www.alliancegenome.org/), which limits their work to a selection of model organisms. @carlocolantuoni has m…
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I run the following code and still get an error message.
Using other mirror sites does not work.
Please let me know how to deal with this error.
```
ensembl
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The 5' and 3' markers on the fusion plot seems to be off. See [the plot here](https://bioconductor.org/packages/devel/bioc/vignettes/chimeraviz/inst/doc/chimeraviz-vignette.html#fusion-plot).
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There is probably some way to do this in general for any annotation in BioConductor. It is easy to do using `biomaRt` for Ensembl, but that's insufficient.
It's probably best to keep this functionali…