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Dear developers,
I have installed and tested ShortStack using your test data. Everything worked perfectly. I just need a little confirmation.
For my analysis I will only need siRNAs. For this reas…
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- Cutadapt and Python version
v2.1.0 with python v3.6.1
- How you installed the tool (conda or pip, for example)
using pip
- Which command-line parameters you used
```
cutadapt -b ADP1 -b ADP2 -…
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@schultzn commented on [Fri Oct 19 2018](https://github.com/cBioPortal/cbioportal/issues/5048)
The term sequenced tumors is misleading. To be consistent with what we use in the study view, we should …
jjgao updated
4 years ago
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Hi,
I have troubles in making getMiRsites to work. the checkProjectFolder() returned check 0.
> check check
[1] 0
My miRs.txt contains 1235 mmu miRbase IDs, e.g.
id
>mmu-let-7g
>mmu-let…
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Hi,
I am wondering if miRDeep2 is able to analyze paired-end reads? I hope I didn't overlooked it in the documentation but so far I didn't see any example for paired-end reads.
Thanks in advance…
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Hi,
After running mirdeep2 and predicting microRNAs I've realised the 3 bed files have exactly the same positions:
examples:
**mature bed file**
LQNS02278089.1 **848170 848230** LQNS02278089.…
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**Submitting author:** @TomKellyGenetics (S. Thomas Kelly)
**Repository:** https://github.com/TomKellyGenetics/graphsim
**Version:** v1.0.0-joss
**Editor:** @majensen
**Reviewer:** @rcannood, @corybru…
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R/Python function:
Input: csv file with the sequences and the secondary structure:
```
"comment","sequence","realmiRNA","secstructure",
"mmu-mir-380 MI0000797 Mus musculus miR-380 stem-loop","AAGA…
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R function:
Input: csv file with the sequences:
```
"comment","sequence","realmiRNA"
"mmu-mir-380 MI0000797 Mus musculus miR-380 stem-loop","AAGAUG",1
"mmu-mir-381 MI0000798 Mus musculus miR-381 …
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**Submitting author:** @TomKellyGenetics (S. Thomas Kelly)
**Repository:** https://github.com/TomKellyGenetics/graphsim
**Version:** 0.1.2
**Editor:** @majensen
**Reviewers:** @rcannood, @corybrunson
…