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Showing :
GRanges
•
reset
9
votes
38
replies
8.2k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.8 years ago by
tangming2005
▴ 200
0
votes
1
reply
799
views
GRanges list convert into igraph format
GRanges
igraph
updated 22 months ago by
Lluís Revilla Sancho
▴ 760 • written 22 months ago by
Bogdan
▴ 670
3
votes
1
reply
907
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges
GenomicRanges
updated 23 months ago by
Michael Love
43k • written 23 months ago by
d.s.h.andel-3
• 0
2
votes
1
reply
2.4k
views
Removing metadata rows containing NA values in GRanges
IRanges
GRanges
NA
updated 2.2 years ago by
ATpoint
★ 4.6k • written 2.2 years ago by
Timucin
• 0
2
votes
5
replies
1.9k
views
Merge GRanges, ignore strand
Sequencing
SummarizedExperiment
GRanges
2.3 years ago
Marcus
• 0
1
vote
1
reply
1.1k
views
lapply for GRanges
lapply
GRanges
updated 2.5 years ago by
Hervé Pagès
16k • written 2.5 years ago by
16301050225
• 0
2
votes
2
replies
2.7k
views
Feature request: syntax for dropping unused seqlevels in GRanges objects
granges
seqlevels
feature request
updated 2.5 years ago by
story.benjamin
▴ 20 • written 7.6 years ago by
Charles Plessy
▴ 180
0
votes
2
replies
1.5k
views
cannot install various functions in R
GRanges
packages
installation
updated 2.6 years ago by
shepherl
4.1k • written 2.6 years ago by
Eli
• 0
1
vote
2
replies
1.1k
views
How to apply a function to a RleViesList object?
Views
IRanges
GRanges
RleList
updated 3.2 years ago by
Mike Smith
★ 6.6k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.3k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
3.3 years ago • updated 3.2 years ago
Arslan
• 0
0
votes
5
replies
3.6k
views
Grange object subsetting using seqnames
Seqnames
makeGRangesFromDataFrame
GRanges
Subsetting
GenomicRanges
3.4 years ago
rtrivedi1
▴ 10
0
votes
1
reply
1.9k
views
annotateWithGeneParts
GRanges
updated 3.5 years ago by
Malcolm Cook
★ 1.6k • written 3.5 years ago by
Punjika
• 0
1
vote
2
replies
1.2k
views
Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges
ORFik
openreadingframe
circulargenome
findORFsFasta
updated 3.7 years ago by
hauken_heyken
▴ 80 • written 3.7 years ago by
levasseurmaxence
• 0
16
votes
19
replies
21k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 2.8 years ago by
Nadine
▴ 60 • written 10.1 years ago by
Darya Vanichkina
▴ 130
1
vote
3
replies
2.6k
views
Merging Neighboring Genomic Segments
Granges
GenomicRanges
4.1 years ago
rahnaman
▴ 10
0
votes
4
replies
1.5k
views
Gene information (GRanges + sequence) to GenBank
granges
genomic ranges
genbankr
ensembldb
updated 4.1 years ago by
James W. MacDonald
67k • written 4.1 years ago by
biomiha
▴ 20
0
votes
1
reply
1.1k
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR
granges
iranges
updated 4.1 years ago by
bernatgel
▴ 150 • written 4.6 years ago by
Angel Liang
• 0
10
votes
3
replies
5.4k
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 4.3 years ago by
merv
▴ 140 • written 4.3 years ago by
deepue
▴ 10
3
votes
7
replies
1.7k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges
GenomicRanges
GenomicFeatures
cdsByOverlaps
DiffBind
updated 4.3 years ago by
James W. MacDonald
67k • written 4.3 years ago by
vanbelj
▴ 30
8
votes
10
replies
2.4k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges
IRanges
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
omarrafiqued
▴ 50
2
votes
2
replies
1.5k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 4.6 years ago by
Hervé Pagès
16k • written 4.6 years ago by
Robert
▴ 10
1
vote
1
reply
2.7k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer
genomicranges
granges
updated 4.7 years ago by
Michael Lawrence
★ 11k • written 4.7 years ago by
ssabri
▴ 20
7
votes
16
replies
4.0k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores
granges
phastCons100way.UCSC.hg38
r
rtracklayer
updated 21 days ago by
rania.alanany
• 0 • written 4.7 years ago by
Biologist
▴ 120
0
votes
6
replies
2.5k
views
GenomicRanges: Find first, second and third nearest genes
R
GenomicRanges
Granges
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
ssabri
▴ 20
0
votes
1
reply
1.3k
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor
biostrings
gc content
biostring
granges
updated 5.1 years ago by
Hervé Pagès
16k • written 5.1 years ago by
atotalamateur
• 0
3
votes
12
replies
2.5k
views
Understanding group_by, reduce_ranges,
plyranges
granges
updated 5.1 years ago by
lee.s
▴ 70 • written 5.1 years ago by
Konstantinos Yeles
▴ 80
4
votes
9
replies
1.8k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges
granges
grangeslist
R
updated 5.2 years ago by
James W. MacDonald
67k • written 5.2 years ago by
new_user6
• 0
8
votes
8
replies
8.8k
views
How to remove out of bound rows from granges
Granges
grangeslist
updated 5.4 years ago by
balwierz
▴ 40 • written 9.2 years ago by
vinod.acear
▴ 50
3
votes
10
replies
8.0k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges
GRanges
5.4 years ago
Robert
▴ 10
4
votes
2
replies
1.3k
views
Build GPos from IPos
genomicranges
granges
gpos
updated 5.5 years ago by
Hervé Pagès
16k • written 6.2 years ago by
maltethodberg
▴ 180
0
votes
2
replies
2.9k
views
GenomicRanges error constructing Granges
granges
updated 5.7 years ago by
James W. MacDonald
67k • written 5.7 years ago by
rhooads7
• 0
2
votes
1
reply
1.1k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb
GRanges
BSGenome
variant annotation
updated 5.7 years ago by
James W. MacDonald
67k • written 5.7 years ago by
jacorvar
▴ 40
4
votes
1
reply
1.4k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges
seqinfo
import.bw
BigWigFile
rtracklayer
updated 5.7 years ago by
Michael Lawrence
★ 11k • written 5.7 years ago by
maltethodberg
▴ 180
1
vote
3
replies
1.4k
views
Obtain coordinates of 5' upstream region up to closest coding region
r
granges
promoter
updated 5.8 years ago by
Hervé Pagès
16k • written 5.8 years ago by
eggrandio
• 0
2
votes
1
reply
1.6k
views
Create a matrix to show overlaps among multiple GRanges
r
GRanges
GenomicRanges
updated 5.8 years ago by
James W. MacDonald
67k • written 5.8 years ago by
Vinicius Henrique da Silva
▴ 40
3
votes
2
replies
2.1k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges
ChIPseeker
annotatePeak
TxDb
EnsDb
updated 5.8 years ago by
Johannes Rainer
★ 2.1k • written 5.8 years ago by
foehn
▴ 100
6
votes
8
replies
3.3k
views
Ranges from a fasta file
biostrings
fasta
genomicranges
granges
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
Konstantinos Yeles
▴ 80
0
votes
4
replies
1.3k
views
Change sign from Granges scores to visualize negative strand data
granges
rtracklayer
updated 5.8 years ago by
James W. MacDonald
67k • written 5.8 years ago by
ferbecneu
• 0
6
votes
12
replies
2.2k
views
mclapply to loop over a GRangesList object
GenomicRanges
GRanges
GRangesList
parallel
mclapply
5.8 years ago
foehn
▴ 100
0
votes
1
reply
1.1k
views
Creating GRanges object
microarray
minfi
GenomicRatio
GRanges
Methylation
updated 5.9 years ago by
James W. MacDonald
67k • written 5.9 years ago by
lalchungnungabt17
• 0
2
votes
4
replies
1.7k
views
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
txdb
txdb.hsapiens.ucsc.hg19.knowngene
granges
exons
ucsc
updated 6.0 years ago by
James W. MacDonald
67k • written 6.0 years ago by
olavur
▴ 10
0
votes
1
reply
889
views
How is it possible to override the constructor of the GRanges class?
genomicranges
granges
6.0 years ago
Shaurya Jauhari
• 0
5
votes
8
replies
9.8k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges
genomicranges
iranges
subsetByOverlaps
updated 2.8 years ago by
b.simpson
• 0 • written 9.2 years ago by
vinod.acear
▴ 50
1
vote
2
replies
1.1k
views
Obtain GRanges object by gene names
GRanges
gene symbol
IdeoViz
6.0 years ago
Arman Shahrisa
▴ 20
2
votes
4
replies
1.7k
views
Split GRanges to GRangeList based on mcols value
granges
updated 6.1 years ago by
Michael Lawrence
★ 11k • written 6.1 years ago by
unamourdeswann
▴ 10
1
vote
2
replies
1.4k
views
Split AME .tsv file into GRanges object or DataFrame
meme
ame
motif
dataframe
granges
updated 6.1 years ago by
Michael Lawrence
★ 11k • written 6.1 years ago by
rbronste
▴ 60
2
votes
1
reply
1.2k
views
Intra-range transformation on GPos-objects?
genomicranges
gpos
granges
updated 6.2 years ago by
Hervé Pagès
16k • written 6.2 years ago by
maltethodberg
▴ 180
0
votes
3
replies
2.9k
views
Selecting columns form a list of grange objects
r
granges
grange
6.2 years ago
g.k
• 0
2
votes
2
replies
4.5k
views
Concatenate a list of genomic ranges
r
granges
genomicranges
updated 6.2 years ago by
James W. MacDonald
67k • written 6.2 years ago by
g.k
• 0
4
votes
8
replies
1.8k
views
the closest gene to a breakpoint
granges
plyranges
updated 6.3 years ago by
Gordon Smyth
52k • written 6.3 years ago by
Bogdan
▴ 670
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Thank you for your detailed answer, I appreciate it and your work.
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