User: maltethodberg

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maltethodberg130
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130
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Posts by maltethodberg

<prev • 70 results • page 1 of 7 • next >
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Answer: A: Genome database and transcription database have different lengths
... You are correct, CAGEfightR is complaining that the two genomes (obtained via seqinfo()/seqlengths() ) are not identical. I have seen a couple of people having similar problems, so CAGEfightR is probably currently a bit too strict in enforcing this. We will probably remove this error in future versi ...
written 4 days ago by maltethodberg130
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Comment: C: CAGEFightR to get CTSS from CAGE error
... This could be an issue with the BigWig-input files. CAGEfightR assumes all ranges in the BigWig is exactly 1, i.e. a single count for each single basepair (traditional CTSS format). This could be checked using something like this: `gr <- import(bw_file)` `table(width(gr))` ...
written 10 weeks ago by maltethodberg130
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Comment: C: Adding a legend to a GeneRegionTrack?
... The use case was manually setting colors of items on a GeneRegionTrack, for example colouring by strand. I figured a somewhat hacky workaround: You can use an OverlayTrack, to put a DataTrack with no data but a legend on top of a GeneRegionTrack. You have to do some fiddling to make sure the feature ...
written 3 months ago by maltethodberg130
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Adding a legend to a GeneRegionTrack?
... Quick Gviz question: For a DataTrack, there is an option to add a legend via setting legend=TRUE I'm using the feature argument in GeneRegionTrack to color different features. Is there a way to add a legend to the track indicating what the colors mean? Simply supplying legend=TRUE does not work. ...
gviz generegiontrack written 4 months ago by maltethodberg130
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What's the recommended way to overwrite the seqinfo of a GRanges?
... I'm having some difficulties when using rtracklayer to import BigWig-files: import.bed includes the genome argument, which correctly sets the seqinfo on the resulting GRanges. However, import.bw does not have a similar argument; The resulting GRanges will have the seqinfo stored in the BigWigFile. ...
rtracklayer granges import.bw seqinfo bigwigfile written 4 months ago by maltethodberg130 • updated 4 months ago by Michael Lawrence11k
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Comment: C: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... Thanks for the detailed comment! I don't think the the two-stage approach you suggest would be entirely appropriate here, as the two timepoints have a very different number of pairwise differences (more than twice as many difference between sites on the segment time point). Would it still be correc ...
written 6 months ago by maltethodberg130
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Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... I'm analysing an RNA-Seq dataset with the following study design: Three locations (e.g. A, B, C) at two different times (e.g. time 1 and 2), everything in triplicates. I'm interested in finding DE genes within each time point: A1 vs B1, A1 vs C1, B1 vs C1, and similarly for the second time point. I ...
limma decidetests stager written 6 months ago by maltethodberg130 • updated 6 months ago by Koen Van den Berge170
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Comment: C: Best way of creating a large RleMatrix
... Thank you! Does the new constructor affect how the chunks are structured? If you construct an RleMatrix from a DataFrame of Rle's, is the RleMatrix then chunked by column? ...
written 6 months ago by maltethodberg130
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Best way of creating a large RleMatrix
... What's the preferred way of creating a large RleMatrix? The documentation page ?RleMatrix only covers how make an RleMatrix from a single Rle (which doesn't work for very large RleMatrix objects) First creating a normal matrix and then coercing to RleMatrix, requires keeping the original matrix in ...
delayedarray rlematrix written 8 months ago by maltethodberg130 • updated 6 months ago by Hervé Pagès ♦♦ 14k
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Comment: C: bplapply with progressbar
... Picking up on this answer, is it possible to have bpapply show a progress bar similar to pbapply when using SerialCoreParam? ...
written 8 months ago by maltethodberg130

Latest awards to maltethodberg

Scholar 4 days ago, created an answer that has been accepted. For A: Genome database and transcription database have different lengths
Voter 6 months ago, voted more than 100 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Popular Question 9 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Student 11 months ago, asked a question with at least 3 up-votes. For Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 3.2 years ago, voted at least 25 times.

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