User: maltethodberg

gravatar for maltethodberg
maltethodberg110
Reputation:
110
Status:
Trusted
Location:
UCPH
Last seen:
2 days, 18 hours ago
Joined:
3 years, 3 months ago
Email:
m************@gmail.com

Posts by maltethodberg

<prev • 69 results • page 1 of 7 • next >
0
votes
0
answers
42
views
0
answers
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 13 days ago by maltethodberg110
0
votes
0
answers
65
views
0
answers
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 6 weeks ago by maltethodberg110
0
votes
0
answers
65
views
0
answers
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 10 weeks ago by maltethodberg110
4
votes
1
answer
88
views
1
answer
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 10 weeks ago by maltethodberg110 • updated 10 weeks ago by Michael Lawrence11k
0
votes
1
answer
147
views
1
answers
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 4 months ago by maltethodberg110
4
votes
1
answer
147
views
1
answer
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 4 months ago by maltethodberg110 • updated 4 months ago by Koen Van den Berge170
0
votes
1
answer
205
views
1
answers
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 4 months ago by maltethodberg110
4
votes
1
answer
205
views
1
answer
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 6 months ago by maltethodberg110 • updated 4 months ago by Hervé Pagès ♦♦ 13k
0
votes
1
answer
226
views
1
answers
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 6 months ago by maltethodberg110
0
votes
1
answer
231
views
1
answers
Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Thanks for the detailed response! I'm considering updating the CAGEfightR-package from using dgCMatrix to using DelayedArray instead (giving the new addition of parallel processing and quick summaries from DelayedMatrixStats, particularly rowsum). Using RleMatrix seems like the obvious choice for re ...
written 6 months ago by maltethodberg110

Latest awards to maltethodberg

Popular Question 6 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Popular Question 7 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Student 9 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 23 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Popular Question 23 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 3.1 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 186 users visited in the last hour