Showing : GRanges • reset
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 17 days ago by • 0 • written 8.0 years ago by ▴ 180
9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.2 years ago by ▴ 190
0
votes
1
reply
620
views
GRanges list convert into igraph format
GRanges igraph
updated 15 months ago by ▴ 730 • written 15 months ago by ▴ 670
3
votes
1
reply
707
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 16 months ago by 41k • written 16 months ago by • 0
2
votes
1
reply
1.8k
views
Removing metadata rows containing NA values in GRanges
IRanges GRanges NA
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
2
votes
5
replies
1.4k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
20 months ago Marcus • 0
1
vote
1
reply
859
views
lapply for GRanges
lapply GRanges
updated 23 months ago by 16k • written 23 months ago by • 0
2
votes
2
replies
2.4k
views
Feature request: syntax for dropping unused seqlevels in GRanges objects
granges seqlevels feature request
updated 23 months ago by ▴ 20 • written 7.0 years ago by ▴ 180
0
votes
2
replies
1.1k
views
cannot install various functions in R
GRanges packages installation
updated 24 months ago by 3.8k • written 24 months ago by • 0
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 2.1 years ago by 16k • written 7.9 years ago by ▴ 40
5
votes
8
replies
8.8k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.2 years ago by • 0 • written 8.6 years ago by ▴ 50
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 2.2 years ago by ▴ 60 • written 9.5 years ago by ▴ 120
6
votes
11
replies
7.3k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 2.4 years ago by ▴ 40 • written 8.3 years ago by ▴ 80
1
vote
2
replies
925
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 2.6 years ago by ★ 6.5k • written 2.6 years ago by ★ 1.5k
0
votes
2
replies
1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.6 years ago Arslan • 0
0
votes
5
replies
2.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.8 years ago rtrivedi1 ▴ 10
0
votes
1
reply
1.4k
views
annotateWithGeneParts
GRanges
updated 2.9 years ago by ★ 1.6k • written 2.9 years ago by • 0
1
vote
2
replies
976
views
Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges ORFik openreadingframe circulargenome findORFsFasta
updated 3.1 years ago by ▴ 80 • written 3.1 years ago by • 0
1
vote
3
replies
1.9k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
3.5 years ago • updated 3.4 years ago rahnaman ▴ 10
0
votes
4
replies
1.2k
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 20
0
votes
1
reply
892
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 3.5 years ago by ▴ 150 • written 4.0 years ago by • 0
8
votes
3
replies
3.9k
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 3.7 years ago by ▴ 120 • written 3.7 years ago by ▴ 10
3
votes
7
replies
1.5k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 30
8
votes
10
replies
1.9k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 50
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 10
1
vote
1
reply
2.2k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.1 years ago by ★ 11k • written 4.1 years ago by ▴ 20
7
votes
13
replies
2.5k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4.1 years ago by ★ 3.3k • written 4.1 years ago by ▴ 110
0
votes
6
replies
1.9k
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 4.5 years ago by 16k • written 4.5 years ago by • 0
3
votes
12
replies
2.0k
views
Understanding group_by, reduce_ranges,
plyranges granges
updated 4.5 years ago by ▴ 70 • written 4.5 years ago by ▴ 80
4
votes
9
replies
1.6k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
8
votes
8
replies
8.1k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 4.8 years ago by ▴ 40 • written 8.5 years ago by ▴ 50
3
votes
10
replies
6.8k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.8 years ago Robert ▴ 10
4
votes
2
replies
1.1k
views
Build GPos from IPos
genomicranges granges gpos
updated 4.9 years ago by 16k • written 5.6 years ago by ▴ 180
0
votes
2
replies
2.5k
views
GenomicRanges error constructing Granges
granges
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
2
votes
1
reply
885
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 40
4
votes
1
reply
1.1k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 5.1 years ago by ★ 11k • written 5.1 years ago by ▴ 180
1
vote
3
replies
1.2k
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 5.2 years ago by 16k • written 5.2 years ago by • 0
2
votes
1
reply
1.4k
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 5.2 years ago by 65k • written 5.2 years ago by ▴ 40
3
votes
2
replies
1.7k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.2 years ago by ★ 2.0k • written 5.2 years ago by ▴ 100
6
votes
8
replies
2.7k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 80
0
votes
4
replies
1.1k
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
6
votes
12
replies
1.8k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.2 years ago foehn ▴ 100
0
votes
1
reply
922
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
2
votes
4
replies
1.4k
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 5.4 years ago by 65k • written 5.4 years ago by ▴ 10
0
votes
1
reply
767
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
5.4 years ago Shaurya Jauhari • 0
1
vote
2
replies
934
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
5.4 years ago Arman Shahrisa ▴ 20
2
votes
4
replies
1.3k
views
Split GRanges to GRangeList based on mcols value
granges
updated 5.5 years ago by ★ 11k • written 5.5 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Split AME .tsv file into GRanges object or DataFrame
meme ame motif dataframe granges
updated 5.5 years ago by ★ 11k • written 5.5 years ago by ▴ 60
2
votes
1
reply
1000
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 180
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Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
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You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
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SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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