Showing : intersect • reset
5
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9
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8.9k
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subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 670
2
votes
8
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5.2k
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GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
6.2 years ago Caroline Grisbach Meissner ▴ 10
6
votes
2
replies
4.7k
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How to get the intersect and get the difference of a grange object while keeping meta data
genomicranges intersect
updated 7.9 years ago by 3.8k • written 7.9 years ago by ▴ 30
0
votes
4
replies
3.3k
views
[Solved]Preserve metadata column for retrieving common regions from two GRanges objects
granges intersect
8.1 years ago Jurat Shahidin ▴ 80
0
votes
9
replies
2.7k
views
IRanges: reduce(), findOverlaps(), and intersect() by group
iranges findoverlaps intersect group
8.3 years ago pesquivel • 0
3
votes
5
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1.6k
views
Extract coordinates of overlapping genomic intervals
genomicranges findoverlaps intersect
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 110
0
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1
reply
885
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 6.9 years ago by 16k • written 6.9 years ago by • 0
0
votes
2
replies
876
views
feel confused when identifying overlapping regions by intersect method
GenomicRanges overlaps intersect
updated 5.1 years ago by ★ 11k • written 5.1 years ago by • 0
5
votes
2
replies
539
views
Intersecting two big dataframe
genomicrange intersect
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 30
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Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by Michael Love 41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Answer: covariate with negative and positive values by Michael Love 41k
Not a problem. However, if the values are very large (eg 1e6) or very small (eg 1e-6), it's a good idea to center and scale the variable…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist by Sherin • 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
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Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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