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subsetbyoverlaps
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
2.5 years ago
Laureano Tomás-Daza
▴ 10
9
votes
9
replies
5.3k
views
Subset GRanges by intersection
findOverlaps
GPos
GenomicRanges
subsetByOverlaps
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
Robert
▴ 10
2
votes
3
replies
2.7k
views
subsetByOverlaps with Multimapping
genomicranges
subsetbyoverlaps
granges
findoverlaps
8.4 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
2.3k
views
I want have a score vector of length of grange that is overlapping with other grange.
granges
findoverlaps
subsetbyoverlaps
updated 10.2 years ago by
Michael Lawrence
★ 11k • written 10.2 years ago by
vinod.acear
▴ 50
3
votes
2
replies
2.2k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges
genomicranges
findoverlaps
subsetbyoverlaps
updated 10.2 years ago by
Hervé Pagès
16k • written 10.2 years ago by
vinod.acear
▴ 50
5
votes
8
replies
11k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges
genomicranges
iranges
subsetByOverlaps
updated 3.9 years ago by
b.simpson
• 0 • written 10.3 years ago by
vinod.acear
▴ 50
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Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
JKim
• 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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