Showing : Granges • reset
0
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623
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
714
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
861
views
lapply for GRanges
lapply GRanges
updated 23 months ago by 16k • written 23 months ago by • 0
0
votes
2
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1.1k
views
cannot install various functions in R
GRanges packages installation
updated 2.0 years ago by 3.9k • written 2.0 years ago by • 0
1
vote
2
replies
929
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
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2
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1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.7 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
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1
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1.4k
views
annotateWithGeneParts
GRanges
updated 3.0 years ago by ★ 1.6k • written 3.0 years ago by • 0
1
vote
2
replies
981
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
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3
replies
1.9k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
3.5 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
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
0
votes
1
reply
896
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 3.6 years ago by ▴ 150 • written 4.0 years ago by • 0
1
vote
1
reply
2.3k
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
2.6k
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 4.7 years ago by 65k • written 4.7 years ago by • 0
3
votes
10
replies
6.8k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.8 years ago Robert ▴ 10
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
888
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 5.2 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
2.8k
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
1.9k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.2 years ago foehn ▴ 100
0
votes
1
reply
927
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
772
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
937
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
5.5 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
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
2
votes
1
reply
1.0k
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 180
0
votes
3
replies
2.4k
views
Selecting columns form a list of grange objects
r granges grange
5.6 years ago g.k • 0
2
votes
2
replies
3.9k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
1
reply
1.6k
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
5.7 years ago jerrywu1987 • 0
4
votes
8
replies
1.5k
views
the closest gene to a breakpoint
granges plyranges
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 670
5
votes
9
replies
9.1k
views
subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 670
1
vote
1
reply
971
views
Subsetting GRanges objext
GRanges subsetting
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
0
votes
7
replies
2.2k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
2
votes
1
reply
1.3k
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Comment: fgsea significant result by Chris • 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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