Showing : findoverlaps • reset
9
votes
9
replies
2.3k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 20 months ago by 63k • written 20 months ago by ▴ 10
2
votes
3
replies
895
views
Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
4.0 years ago O. William McClung • 0
7
votes
5
replies
3.3k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 4.9 years ago by • 0 • written 6.0 years ago by ★ 1.5k
0
votes
3
replies
863
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
5.0 years ago francesca casalino ▴ 50
0
votes
1
reply
748
views
R_Granges_adding merged Metadata columns
granges findoverlaps
5.5 years ago me.saichi • 0
2
votes
8
replies
4.7k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
5.7 years ago Caroline Grisbach Meissner ▴ 10
2
votes
3
replies
1.7k
views
subsetByOverlaps with Multimapping
genomicranges subsetbyoverlaps granges findoverlaps
6.1 years ago Assa Yeroslaviz ★ 1.5k
0
votes
10
replies
1.7k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
6.3 years ago lovro0 ▴ 10
1
vote
1
reply
748
views
Obtain exactly the interval that overlap
findoverlaps Granges
updated 6.4 years ago by 11k • written 6.4 years ago by ▴ 30
2
votes
2
replies
992
views
Findoverlaps insame sample
genomicranges granges findoverlaps
6.4 years ago julrodr80 ▴ 30
0
votes
1
reply
1.1k
views
findOverlaps - how to get adjacent ranges?
findOverlaps IRanges
updated 6.5 years ago by 11k • written 6.5 years ago by ▴ 20
0
votes
3
replies
1.6k
views
findOverlaps() error after updating package
GenomicRanges findOverlaps
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 20
1
vote
4
replies
937
views
pROBLEMS WITH findOverlapPairs
gRANGES iranges findoverlaps
updated 6.6 years ago by 63k • written 6.6 years ago by ▴ 30
2
votes
7
replies
1.8k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
6.8 years ago lovro0 ▴ 10
1
vote
12
replies
1.8k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r iranges findoverlaps IntegerList List
7.1 years ago • updated 6.9 years ago jian_liangli • 0
5
votes
2
replies
1.2k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.2 years ago • updated 6.9 years ago Jurat Shahidin ▴ 80
3
votes
3
replies
968
views
Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
IRanges GRanges findoverlaps R
updated 7.1 years ago by 11k • written 7.1 years ago by • 0
3
votes
5
replies
1.4k
views
Extract coordinates of overlapping genomic intervals
genomicranges findoverlaps intersect
updated 7.1 years ago by 13k • written 7.1 years ago by ▴ 110
2
votes
2
replies
1.1k
views
GRanges get hits from (only) antisense strand with findOverlaps().
GRanges findoverlaps antisense
updated 7.1 years ago by ▴ 450 • written 7.1 years ago by • 0
3
votes
9
replies
1.5k
views
find next non-overlapping nth elements of a given region
biomart granges findoverlaps
updated 7.3 years ago by 11k • written 7.3 years ago by ▴ 20
28
votes
43
replies
7.4k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 7.4 years ago by 25k • written 7.6 years ago by ▴ 80
0
votes
6
replies
1.4k
views
Is that an efficient way to find the overlapped , upstream and downstream genes for a bunch of genes
genomicranges geneoverlap findoverlaps
updated 7.5 years ago by 11k • written 7.5 years ago by • 0
6
votes
7
replies
1.5k
views
How to implement element-wise-overlaps with iteration for two different bed files in R?
r findoverlaps iterators
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 80
0
votes
9
replies
2.3k
views
IRanges: reduce(), findOverlaps(), and intersect() by group
iranges findoverlaps intersect group
7.8 years ago pesquivel • 0
0
votes
3
replies
1.5k
views
I want have a score vector of length of grange that is overlapping with other grange.
granges findoverlaps subsetbyoverlaps
updated 7.9 years ago by 11k • written 7.9 years ago by ▴ 50
0
votes
0
replies
952
views
Different amount of overlapping Peaks in ChIPpeakAnno-Package
chippeakanno findoverlaps venn diagram
7.9 years ago N. F. • 0
8
votes
3
replies
3.9k
views
how to extract Granges not overlapping with other ganges?
Granges findoverlaps
updated 7.9 years ago by 63k • written 7.9 years ago by ▴ 50
3
votes
2
replies
1.3k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 7.9 years ago by 16k • written 7.9 years ago by ▴ 50
2
votes
5
replies
1.8k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 8.0 years ago by 16k • written 8.1 years ago by ▴ 150
3
votes
7
replies
1.7k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 8.1 years ago by 16k • written 8.1 years ago by ▴ 150
1
vote
1
reply
1.3k
views
Using findOverlaps to find only partial overlaps
findoverlaps genomicranges
updated 8.1 years ago by 11k • written 8.1 years ago by ▴ 150
1
vote
1
reply
1.2k
views
Performing findOverlaps when both subject and query are on the order of a million
findoverlaps
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 30
3
votes
5
replies
2.7k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
8.6 years ago summerela • 0
10
votes
8
replies
2.3k
views
Transitive overlaps of GRanges object
granges findOverlaps
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 40
34 results • Page 1 of 1
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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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