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Thank you so much for this useful package.
When running `isoAnnotate` I encountered the following error:
```
Error in `[[
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The `mirtop.tsv` output contains repeated rows for some isomiRs with identical first 12 columns:
```
UID Read miRNA Variant iso_5p iso_3p iso_add3p iso_snp iso_5p_nt iso_3p_nt iso_add3p_…
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Hi Lorena,
Thanks once again for this useful package. I have a question which is more biological I guess. So, after getting the counts file if I look at the mature miRNA (ref) and isomiRs separately …
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Hi there,
Thank you very much for this useful R package.
I am trying to use scanMiR to identify mRNA targets when using isomiRs.
I can use findSeedMatches given any miRNA sequence, either canon…
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I installed mirtop v 0.4.22 to process the mirGFF output files generated by miRge2.0. I tried it with miniconda2 (python v2.7) as well as python v3.6 in ubuntu wsl.
When running `$ mirtop stats`, a…
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Hi,
I have problem running Bioconductor isomiRs package using conda. Specifically version 1.14, 1.16, 1.18 (tried all of them), previous versions (1.8, 1.10) work ok. When I install isomiRs locally…
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Hi there
Thanks for the great package.
I was wondering if there is a way to map back isomiRs with known SNPs to their respective rsIDs or other variant nomenclature/genomic coordinate?
For e…
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Implement option in `stats` sub-command like `--detail` to:
[ ] show distribution of sequences per sample (geom_density)
[ ] boxplot distribution per sample after normalization like DESeq2
[ ] su…
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When using `isoCounts` function with different isomiR types set to `TRUE`, it seems the counts for that type is added to the original counts matrix in the object:
```
ids_counts_all = isoCounts(is…
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Please, describe below the problem you think we face in the miRNA/isomiR naming.
Try to summarize it in 200 words. The current discussions are here:
* isomirs : https://github.com/miRTop/incubat…