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Deal with duplicated entries. Issue illustrated in the README plot (loci chr4Hg0380431, chr4Hg0383761, or chr5Hg0547031).
Duplicated _loci_ are _locus_ id that appears more than once in the annotat…
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Thanks for a great easy to use tool. I've finally reached the step where I would like to do a Gene Centric Noncoding conditional analysis on some select rare variants I identified in my data set.
As…
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Hello Mr. Tom Doel
I am Amir Zamanpour, I am medical imaging student at Mashhad university of medical science. first of all, thanks for your useful app(Pulmonary Toolkit), I want to use it for proces…
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Hello,
I was reviewing the script in your repository and I came across a line where null="null.bed" is assigned. I'm trying to understand the purpose of this file and whether it needs to be created…
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Integrate Arabidopsis transcription factor database into the knowledge network. Visualize the information as part of the gene-evidence networks (see email trail below).
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From: Richard Barker
Se…
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Hello,
I have defined annotation features - promoter and enhancer lists. I used them with Hi-C data trying to find enhancer-promoter pairs. My Hi-C data ranges were 10kb in size. Later I repeated t…
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Dear Team,
I am calculating Partition heritability , but I am getting error of "parsing annotation error". Can you please help me with this? Here is my command:
GWAS trait: PASS.Bipolar_Disorder_AL…
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It has been a while since I have noticed that a few entries would not be returned despite being present in the genome file.
E.g. I would not get promoters back when querying "chrXHg123456" if the loc…
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Hi~
I got my data(.bam file) at http://atlas.gs.washington.edu/mouse-atac/data/. And I generated snap file using the bam file according to your instruction.
But I don't have a CSV file tha…
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Hi there,
Thanks for keeping up with my questions. As bicycle is able to from differential analysis between two different groups i.e treatment vs control. I wanted to know if bicycle can perform com…