User: s1437643

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s14376430
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Posts by s1437643

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Support for BSgenomeViews objects in matchPWM
... Thank you for the suggestion. I've just opened an issue. ...
written 5 months ago by s14376430
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Support for BSgenomeViews objects in matchPWM
... Would it be possible to add a method for BSgenomeViews objects in the matchPWM function? The manual says it can take ordinary Views objects, but I don't see any support for BSgenomeViews objects? Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘matc ...
biostrings written 5 months ago by s14376430
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Comment: C: One-way hypothesis test in limma
... Many thanks, Aaron. ...
written 6 months ago by s14376430
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One-way hypothesis test in limma
... Is it possible to test for fold-change in only one direction (LFC > 0) using the treat function from limma? Similar to using the altHypothesis argument in the results function from DESeq2? I tried myself to introduce some changes to the code in treat to perform this: lfc <- 0 se <- stdev ...
limma written 6 months ago by s14376430 • updated 6 months ago by Gordon Smyth35k
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Comment: C: Aggregate read counts by non-uniform overlapping sliding windows
... Thanks Aaron, I'll stick with featureCounts to generate the window counts. ...
written 21 months ago by s14376430
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Aggregate read counts by non-uniform overlapping sliding windows
... I have a matrix of read counts which represent the number of reads aligned in bins along the genome. There are millions of bins and they are not all the same length. For each bin I would like to count the number of reads within 5,000 bp either side of the bin's centre. Reads should only be counted f ...
genomicranges granges featurecounts written 21 months ago by s14376430 • updated 21 months ago by Michael Lawrence10k
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Comment: C: Programatically download correct genome wide annotation package for given organi
... That could work - I'd simply have to parse the organism parameter for the first two letters and perform the query search you suggested. ...
written 21 months ago by s14376430
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Programatically download correct genome wide annotation package for given organism/assembly
... I'm looking for a way to programatically download the correct genome wide annotation package given one of the following or a combination of arguments to a script: Organism: Mmusculus Assembly: mm10 The result would be that the org.MM.eg.db package would be downloaded. ...
annotationdbi organismdbi written 21 months ago by s14376430 • updated 21 months ago by Johannes Rainer1.3k
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Removing GC content bias and trended bias from ChIP-seq data
... Note: I originally posted this on Biostars, but was suggested to post here. I am doing DB analysis of ChIP-seq data using the csaw package. It seems I have a small trended bias and possible GC content bias in my data. Below are MA plots showing signal in the merged peaks using CPM normalisation (LH ...
normalization edger cqn chip-seq csaw written 2.0 years ago by s14376430 • updated 2.0 years ago by Aaron Lun21k
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How to retrieve ranges within 1000bp of each range in an IRanges object?
... I have an IRanges object which contains regions of interest and read counts for a given sample in the metadata column. I would like to iterate through each of the regions and get the counts for regions which are within 1,000 bp of the current region. I have tried the following but It is too slow and ...
iranges written 2.8 years ago by s14376430 • updated 2.8 years ago by Michael Lawrence10k

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