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
3.1k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
3
votes
7
replies
2.0k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 150
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
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
1.1k
views
Findoverlaps insame sample
genomicranges granges findoverlaps
6.9 years ago julrodr80 ▴ 30
2
votes
3
replies
1.1k
views
Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
4.5 years ago O. William McClung • 0
8
votes
3
replies
4.3k
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
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 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 50
0
votes
9
replies
2.7k
views
IRanges: reduce(), findOverlaps(), and intersect() by group
iranges findoverlaps intersect group
8.3 years ago pesquivel • 0
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
1
vote
1
reply
1.3k
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
0
votes
6
replies
1.6k
views
Is that an efficient way to find the overlapped , upstream and downstream genes for a bunch of genes
genomicranges geneoverlap findoverlaps
updated 8.0 years ago by ★ 11k • written 8.0 years ago by • 0
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
5
votes
2
replies
1.4k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.7 years ago • updated 7.4 years ago Jurat Shahidin ▴ 80
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
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
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 7.4 years ago jian_liangli • 0
7
votes
5
replies
3.8k
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
1
vote
1
reply
1.5k
views
Using findOverlaps to find only partial overlaps
findoverlaps genomicranges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 150
2
votes
8
replies
5.2k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
6.2 years ago Caroline Grisbach Meissner ▴ 10
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
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
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
1
reply
1.3k
views
findOverlaps - how to get adjacent ranges?
findOverlaps IRanges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 20
1
vote
1
reply
872
views
Obtain exactly the interval that overlap
findoverlaps Granges
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 30
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
2
votes
3
replies
2.0k
views
subsetByOverlaps with Multimapping
genomicranges subsetbyoverlaps granges findoverlaps
6.6 years ago Assa Yeroslaviz ★ 1.5k
0
votes
3
replies
1.1k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
5.5 years ago francesca casalino ▴ 50
0
votes
1
reply
856
views
R_Granges_adding merged Metadata columns
granges findoverlaps
6.1 years ago me.saichi • 0
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
10
replies
2.0k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
6.8 years ago lovro0 ▴ 10
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Comment: DEG with low counts by Rajat • 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for your guide! I check my data as you said there is no difference in my data. This is the MDS plot at genes l…
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To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Votes
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
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