Katarzyna Sikora comments

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                                            Katarzyna Sikora

rMats - summary

Hi Ward, are you taking care of this? Best, Katarzyna

fix #785

Hi guys, is this PR still pending, or would you like to close it? Best, Katarzyna

Adding bwa-mem2?

Hi Jean, yes, this sounds like a good idea, Best, Katarzyna

Arima enzymes for Hi-C

Hi guys, is this PR still pending, or would you like to close it? Best, Katarzyna

cutntag peak calling

Hi Leily, is this a feature you are working on? Best, Katarzyna

cutntag peak calling

I'll just tag it as enhancement then, for the time being. Thanks!

does the alignment-free mode work with allelic-mapping bam files? mRNA-seq

No, it's not easily extendible. An option would be to convert allelic bam to fastq, and map to the transcriptome with Salmon. Then, a)DESeq2 on salmon in allelic-mode should be...

Matrix rendering much faster when NOT using the shiny wrapper

else if (! isTRUE(Rowv)) { rowInd

[Request] looping inputs for multiple ChIP-seq comparisons

Hi, for multiple comparisons, the sample sheet would have to look like that: name[\t]condition[\t]group sample1[\t]control[\t]group1 sample2[\t]control[\t]group1 sample3[\t]treatment[\t]group1 sample4[\t]treatment[\t]group1 sample5[\t]control[\t]group2 sample6[\t]control[\t]group2 sample7[\t]treatment[\t]group2 sample8[\t]treatment[\t]group2 In this example, the sample sheet would be...