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hello , sorry to disturb you.
I saw the paper 'Inference of transcription factor binding from cellfree DNA enables tumor subtype prediction and early detection' said "The position was recalculated by…
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Current implementation of ChIP-seq pipeline launches `sicer.sh` and filters its output through the pattern `['*sicer.log', '*.bed', '*rip.csv']`. However, `sicer.sh` used to have its own file filterin…
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During development of a pipeline involving Genrich for integrating ATAC seq with ChIP-Seq for multiple marks, I wish to only call peaks on a few small regions. For this reason, it is desirable to be …
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Rather than selecting matrices based on their matrix-quality curves, I thought that it would be more consistent to select those that best meet the evaluation criterion of the IBIS challenge
> This …
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Any plans to create an R/Bioconductor package (e.g., `epicR`)?
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Long TODO lists don't get done.
We are trying to keep an issue open if a real effort is happening to resolve it.
The below priority list gives a sense of where bcbio is heading in the next two rele…
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Hi,
is there a systematic way to find meaningful cutoffs for -s/-w? How do you decide on these?
Best,
Carsten
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Hello,
I've been debugging an issue where some frames are not transmitted upon write(); the affected frames seem random. I think I've tracked down a partial explanation and a fix, but I'm not sure …
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Hi,
I am new to data analysis, we have been doing CnT for histone modifications and transcription factor. First I used the following alignment parameters:
`--local --very-sensitive-local --no-un…
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Hi,
I have several CUT&RN experiments looking at Histone modifications H3K4me3 (narrow peak) and H3K27me3 (broad peaks) in treated vs untreated cells, and seem to have several instances where the b…