User: s1437643

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s14376430
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Posts by s1437643

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Comment: C: In which order should you detect empty droplets / remove barcode swapping using
... Okay, that's cleared it up for me! I was getting confused because swappedDrops was returning a matrix with less columns (i.e. barcodes) and thought this would interfere with the "all barcodes" bit written in the vignette for emptyDrops. I was then substituting the columns from the cleaned matrix bac ...
written 5 months ago by s14376430
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Comment: C: Support for BSgenomeViews objects in matchPWM
... Thank you for the suggestion. I've just opened an issue. ...
written 16 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 16 months ago by s14376430
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Comment: C: One-way hypothesis test in limma
... Many thanks, Aaron. ...
written 17 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 17 months ago by s14376430 • updated 17 months ago by Gordon Smyth38k
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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 2.7 years 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 2.7 years ago by s14376430 • updated 2.7 years ago by Michael Lawrence11k
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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 2.7 years 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 2.7 years ago by s14376430 • updated 2.7 years ago by Johannes Rainer1.5k
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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 2.9 years ago by s14376430 • updated 2.9 years ago by Aaron Lun24k

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