Showing : findOverlaps • reset
28
votes
43
replies
8.4k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 8.0 years ago by 25k • written 8.2 years ago by ▴ 80
10
votes
8
replies
2.6k
views
Transitive overlaps of GRanges object
granges findOverlaps
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 40
9
votes
9
replies
3.2k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
8
votes
3
replies
4.4k
views
how to extract Granges not overlapping with other ganges?
Granges findoverlaps
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 50
7
votes
5
replies
3.9k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 5.5 years ago by • 0 • written 6.6 years ago by ★ 1.5k
6
votes
7
replies
1.8k
views
How to implement element-wise-overlaps with iteration for two different bed files in R?
r findoverlaps iterators
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 80
5
votes
2
replies
1.4k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.8 years ago • updated 7.5 years ago Jurat Shahidin ▴ 80
3
votes
5
replies
3.0k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
9.2 years ago summerela • 0
3
votes
7
replies
2.0k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 150
3
votes
2
replies
1.5k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 8.5 years ago by 16k • written 8.5 years ago by ▴ 50
3
votes
9
replies
1.8k
views
find next non-overlapping nth elements of a given region
biomart granges findoverlaps
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 20
3
votes
5
replies
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
3
votes
3
replies
1.1k
views
Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
IRanges GRanges findoverlaps R
updated 7.7 years ago by ★ 11k • written 7.7 years ago by • 0
2
votes
2
replies
1.1k
views
Findoverlaps insame sample
genomicranges granges findoverlaps
7.0 years ago julrodr80 ▴ 30
2
votes
5
replies
2.1k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 150
2
votes
8
replies
5.3k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
6.3 years ago Caroline Grisbach Meissner ▴ 10
2
votes
7
replies
2.1k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
7.4 years ago lovro0 ▴ 10
2
votes
2
replies
1.3k
views
GRanges get hits from (only) antisense strand with findOverlaps().
GRanges findoverlaps antisense
updated 7.7 years ago by ▴ 450 • written 7.7 years ago by • 0
2
votes
3
replies
1.1k
views
Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
4.6 years ago O. William McClung • 0
2
votes
3
replies
2.0k
views
subsetByOverlaps with Multimapping
genomicranges subsetbyoverlaps granges findoverlaps
6.7 years ago • updated 6.6 years ago Assa Yeroslaviz ★ 1.5k
1
vote
1
reply
1.5k
views
Using findOverlaps to find only partial overlaps
findoverlaps genomicranges
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 150
1
vote
1
reply
882
views
Obtain exactly the interval that overlap
findoverlaps Granges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 30
1
vote
4
replies
1.1k
views
pROBLEMS WITH findOverlapPairs
gRANGES iranges findoverlaps
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 30
1
vote
1
reply
1.4k
views
Performing findOverlaps when both subject and query are on the order of a million
findoverlaps
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 30
1
vote
12
replies
2.1k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r iranges findoverlaps IntegerList List
7.7 years ago • updated 7.5 years ago jian_liangli • 0
0
votes
1
reply
1.3k
views
findOverlaps - how to get adjacent ranges?
findOverlaps IRanges
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 20
0
votes
3
replies
1.1k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
5.6 years ago francesca casalino ▴ 50
0
votes
0
replies
1.1k
views
Different amount of overlapping Peaks in ChIPpeakAnno-Package
chippeakanno findoverlaps venn diagram
8.5 years ago N. F. • 0
0
votes
3
replies
1.7k
views
findOverlaps() error after updating package
GenomicRanges findOverlaps
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 20
0
votes
6
replies
1.7k
views
Is that an efficient way to find the overlapped , upstream and downstream genes for a bunch of genes
genomicranges geneoverlap findoverlaps
updated 8.1 years ago by ★ 11k • written 8.1 years ago by • 0
0
votes
10
replies
2.0k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
6.9 years ago lovro0 ▴ 10
0
votes
1
reply
865
views
R_Granges_adding merged Metadata columns
granges findoverlaps
6.1 years ago me.saichi • 0
0
votes
9
replies
2.7k
views
IRanges: reduce(), findOverlaps(), and intersect() by group
iranges findoverlaps intersect group
8.4 years ago pesquivel • 0
0
votes
3
replies
1.7k
views
I want have a score vector of length of grange that is overlapping with other grange.
granges findoverlaps subsetbyoverlaps
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ▴ 50
34 results • Page 1 of 1
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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
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I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
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But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
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Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
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Bioconductor 3.19 is Released!
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