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Regarding the KEGG annotation usage error, I have already followed up with #572
Seems like the error comes from not updating R or BiocManager or clusterprofiler..
I am currently using R 4.4, Bioc…
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Hello,
I am trying to perform a GO analysis with clusterProfiler, however I am having problems with OrgDb because it is not supported, could anyone suggest something to resolve this?
```
#ORA…
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Pertains to #901
- [ ] form of ensembl URIs. The slash form is more canonical ie https://identifiers.org/ensembl/ENSMUSG00000019772 not https://identifiers.org/ensembl:ENSMUSG00000019772. Also in…
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Can we also support IDs under annotation-controller?
- [x] `/annotation/dbsnp/[dbsnp_id]`
- [ ] `/annotation/cosmic/[cosmic_id]`
- [ ] `/annotation/hgmd/[hgmd_id]`
We can utilize the following…
jjgao updated
6 years ago
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I recently attended HCA Asia, and an attendee requested that Ensembl transcript IDs would be accepted as feature variables for the count matrix, especially for Smart-Seq data. He noted that the reason…
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I'm trying to use kallisto to visualize read alignment in IGV. I'm using the ensembl FASTA for non-coding RNAs and the ensembl GTF. Initially the GTF transcript IDs didn't match the FASTA IDs (because…
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Dear Azimuth team,
I am facing issues with the function
Azimuth:::ConvertEnsembleToSymbol(mat = mat, species = "human") on Seurat integration using BP cell.
I got this error:
```
Error: You…
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Hello,
currently, I am trying to run IsoformSwitchAnaylzer with Kallisto counts. After successfully using importIsoformExpression() to extract my count data, I wanted to set up the switchAnalyzeRlis…
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I noticed that for some reason salmon does not convert transcript ids to gene ids.
Here is the command that I run:
```
salmon --no-version-check quant -i /cromwell-executions/quant_sample/04b46951-…
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## Describe the issue
Using the --symbol option the hgnc_id is sometimes filled in and sometimes not for certain transcripts in certain variants, depending on what variants come before. I am able to…