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Dear developer,
Good day. Thank you for your development and maintenance of this software.
I was wondering if you could explain about the definitions of different classes of `TisType`?
I see …
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- [x] Misannotated genes (supp table 4a)
- [ ] alternative intron retention (supp table 4d)
- [x] 11 ‘dubious appeared to be translated (did we change these to coding?)
- [x] 3 dubious were tra…
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[simulate_data.txt](https://github.com/dieterich-lab/riboseq-utils/files/1457261/simulate_data.txt)
TE can be estimated using a simulation approach based on modifying real data to introduce diffe…
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Have you ever imply your model on human dataset?
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Hello,
Thanks for developing this really interesting methodology. I have a question that did you remove PCR duplicates when processing single-cell riboseq data?
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Hi! I'm running the following code with some big bam files
```
bam_file
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Hi,
I noticed this issue since the first time of trying the vignette, but as there were important issues, waited to bring this to your attention.
### Issue 1
Following this particular [step](…
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**Describe the bug**
I successfully generated the reference according to "xpresspipe curateReference -o /path/to/reference -f /path/to/reference/genome_fastas -g /path/to/reference/transcripts.gtf"
…
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Hi there,
I installed the apeglm and run deltaTE on your sample data, but it only prints the deltaTE fold changes with list of deltaTE genes in text files, and it gives this error at the end.
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Hi,
Thank you for the recent comment on #167 .
I took your suggestion and this time I tried on a Mac which never had ORFik and installed from GitHub.
There is an error which I have not encoun…