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Are the default options from [bedtools merge](https://bedtools.readthedocs.io/en/latest/content/tools/merge.html) good enough for this use case, or are there other methods we should consider?
@kopa…
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Hi,
I saw previous issues mentioning this, but also saw that the change to FoldChange() was implemented in v1.3.0. I am currently using Signac v1.4.0. I'm not sure if the change is working as inten…
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Hi,
I really like the methodology of PRINT over every other footprinting tool, but at the moment I'm having trouble figuring out how to get output in a format that is comparable to other footprint…
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Hi,
The multi-species nucleotide transformer model appears to be very promising! I'm curious, do you have any plans to pre-train the nucleotide transformer on plant species?
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Hi Mette,
This is only a thought/suggestion (not an issue) pertaining to TOBIAS in general, although currently I only run TOBIAS_snakemake.
I am curious to know if there is any plan by Looso la…
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Please add the prepared scripts to the `bin` directory on the `nextflow` branch and add a short description how they should be put together in this issue.
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Hi,
Various matrices are used in snapatac2's tutorial:
Features: creating a cell by bin matrix containing insertion counts across genome-wide 500-bp bins.
gene activity: generates cell by gene ac…
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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/xxxmichixxx/dinoR
Confirm the following by editin…
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Hi Eric,
I wondering if there is some script to update annotated .gff3 file with gene names. In my gff3 file I have all genes named ORF "ID=Contig10.path1;Name=ORF" Is it possible to use transcriptom…
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貼吧活動：(請查閱 [SARS-CoV-2 Timeline by 2020.02.21](https://github.com/agorahub/_meta/blob/agoran/theagora/sari/Memorandum_2020-02-21_SARS-CoV-2-Timeline_Nathan.pdf?raw=true), by Nathan :cloud: )
- Colla…