Showing : findOverlaps • reset
9
votes
9
replies
4.9k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.6 years ago by 68k • written 3.7 years ago by ▴ 10
2
votes
3
replies
1.5k
views
Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
5.9 years ago O. William McClung • 0
7
votes
5
replies
4.8k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 6.9 years ago by • 0 • written 8.0 years ago by ★ 1.5k
0
votes
3
replies
1.6k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
6.9 years ago francesca casalino ▴ 50
0
votes
1
reply
1.2k
views
R_Granges_adding merged Metadata columns
granges findoverlaps
7.4 years ago me.saichi • 0
2
votes
8
replies
6.3k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
7.6 years ago Caroline Grisbach Meissner ▴ 10
2
votes
3
replies
2.6k
views
subsetByOverlaps with Multimapping
genomicranges subsetbyoverlaps granges findoverlaps
8.0 years ago Assa Yeroslaviz ★ 1.5k
0
votes
10
replies
2.7k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
8.2 years ago lovro0 ▴ 10
1
vote
1
reply
1.2k
views
Obtain exactly the interval that overlap
findoverlaps Granges
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 30
2
votes
2
replies
1.4k
views
Findoverlaps insame sample
genomicranges granges findoverlaps
8.3 years ago julrodr80 ▴ 30
0
votes
1
reply
1.7k
views
findOverlaps - how to get adjacent ranges?
findOverlaps IRanges
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 20
0
votes
3
replies
2.1k
views
findOverlaps() error after updating package
GenomicRanges findOverlaps
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 20
1
vote
4
replies
1.4k
views
pROBLEMS WITH findOverlapPairs
gRANGES iranges findoverlaps
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 30
2
votes
7
replies
2.8k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
8.8 years ago • updated 8.7 years ago lovro0 ▴ 10
1
vote
12
replies
2.8k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r iranges findoverlaps IntegerList List
9.1 years ago • updated 8.8 years ago jian_liangli • 0
5
votes
2
replies
1.7k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
9.1 years ago • updated 8.8 years ago Jurat Shahidin ▴ 80
3
votes
3
replies
1.5k
views
Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
IRanges GRanges findoverlaps R
updated 9.1 years ago by ★ 11k • written 9.1 years ago by • 0
3
votes
5
replies
2.0k
views
Extract coordinates of overlapping genomic intervals
genomicranges findoverlaps intersect
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 110
2
votes
2
replies
1.8k
views
GRanges get hits from (only) antisense strand with findOverlaps().
GRanges findoverlaps antisense
updated 9.1 years ago by ▴ 450 • written 9.1 years ago by • 0
3
votes
9
replies
2.4k
views
find next non-overlapping nth elements of a given region
biomart granges findoverlaps
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 20
28
votes
43
replies
10k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 9.4 years ago by 25k • written 9.5 years ago by ▴ 80
0
votes
6
replies
2.3k
views
Is that an efficient way to find the overlapped , upstream and downstream genes for a bunch of genes
genomicranges geneoverlap findoverlaps
updated 9.4 years ago by ★ 11k • written 9.4 years ago by • 0
6
votes
7
replies
2.3k
views
How to implement element-wise-overlaps with iteration for two different bed files in R?
r findoverlaps iterators
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 80
0
votes
9
replies
3.3k
views
IRanges: reduce(), findOverlaps(), and intersect() by group
iranges findoverlaps intersect group
9.7 years ago pesquivel • 0
0
votes
3
replies
2.1k
views
I want have a score vector of length of grange that is overlapping with other grange.
granges findoverlaps subsetbyoverlaps
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 50
0
votes
0
replies
1.4k
views
Different amount of overlapping Peaks in ChIPpeakAnno-Package
chippeakanno findoverlaps venn diagram
9.8 years ago N. F. • 0
9
votes
3
replies
5.4k
views
how to extract Granges not overlapping with other ganges?
Granges findoverlaps
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 50
3
votes
2
replies
2.1k
views
how much positions overlapped for each pair of the pairs obtained by findoverlap.
granges genomicranges findoverlaps subsetbyoverlaps
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 50
2
votes
5
replies
2.7k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 150
3
votes
7
replies
2.6k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 150
1
vote
1
reply
2.0k
views
Using findOverlaps to find only partial overlaps
findoverlaps genomicranges
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 150
1
vote
1
reply
1.7k
views
Performing findOverlaps when both subject and query are on the order of a million
findoverlaps
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 30
3
votes
5
replies
3.8k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
10.5 years ago summerela • 0
10
votes
8
replies
3.2k
views
Transitive overlaps of GRanges object
granges findOverlaps
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 40
34 results • Page 1 of 1
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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