Comments (4)
SICER2 is apparently just a re-implementation of SICER in python3 that's faster and all, so probably no need for the original SICER.
from peakpeeker.
There's also HMMRATAC for ATAC data, from the MACS author.
from peakpeeker.
We'll start with MACS2 and plan to do MACS1.4.3 and SICER2 as well.
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Genrich also looks very easy to pop in.
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Related Issues (20)
- Write shiny module for chosen OG peak caller HOT 1
- Utilize async to ensure responsiveness of the app as peak calling runs HOT 1
- Find good toy data (ChIP, ATAC, CUTNRUN) and test region HOT 1
- Update README/vignette with basic use info/GIFs of package in use.
- De-uglify MACS2 module UI. HOT 1
- Add MACS module.
- Add SICER2 module.
- Add SPAN peakcaller
- Add post-call score/p-val/FDR filters
- Add PeakRanger callers HOT 1
- Add HMMRATAC caller
- Add JAMM caller
- Add SEACR caller
- Bigwig peak callers
- Add PePr caller
- Implement and test using basilisk to install peakcaller envs.
- Determine which parameters matter/should be added for peak callers of interest HOT 1
- Implement button to add new instance of peak caller. HOT 1
- Actually do peak calling
- Convert bed/narrowPeak/whatever output to GFF HOT 4
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