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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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Hi SABINE developers, thank you for developing and sharing this tool with the community. I managed to install SABINE based on the instructions. However, running ./sabine -check-install gives me the fo…
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Hi Helia,
Thank you again for your suggestions. I applied LongTR to twenty sets of data, and only one set encountered the following issue:
```
Detected 1 BAM/CRAM files
User-specified read gro…
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Hello,
I ran a preliminary experiment to see if the all contexts methylation models work in an unusual system. Basically, I amplified the whole genome to remove any marks, then treated samples with…
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Hello,
I got the result and I have a question. So, from this program, I can get the miRNA which is predicted to bind the mRNA based on the log fold change of genes. The output file is a CSV file of mi…
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**Describe the bug**
Hi, thank you for the wonderful software. I am obtaining a large number of hits with gimme scan even when I pass the -n 1 argument for a bed file that has a single interval. Spec…
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Hi,
I used Megalodon to call CpG with the following command
```
megalodon $FAST5 \
--output-directory $OUT \
--outputs basecalls mappings mod_mappings mods \
--reference $REF \
--devices $GPU…
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In my use case of Basset i've bumped into something that would be super useful. This may already be doable (but i'm not sure how): a method to take in a genomic region, a target cell type and output w…
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- [x] extract 3' UTRs
- [x] Perform NLP analysis
(retrieve for every gene we have the UTR)
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/neurogenomics/MotifPeeker
Confirm the following b…