Showing : gRANGES • reset
0
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623
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GRanges list convert into igraph format
GRanges igraph
updated 15 months ago by ▴ 730 • written 15 months ago by ▴ 670
3
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1
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712
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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
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1
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1.8k
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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
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5
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1.4k
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Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
20 months ago Marcus • 0
1
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1
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861
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lapply for GRanges
lapply GRanges
updated 23 months ago by 16k • written 23 months ago by • 0
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2
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1.1k
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cannot install various functions in R
GRanges packages installation
updated 24 months ago by 3.9k • written 24 months ago by • 0
1
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2
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927
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
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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
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5
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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
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annotateWithGeneParts
GRanges
updated 2.9 years ago by ★ 1.6k • written 3.0 years ago by • 0
1
vote
2
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979
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
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3
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1.9k
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Merging Neighboring Genomic Segments
Granges GenomicRanges
3.5 years ago rahnaman ▴ 10
0
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4
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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
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3
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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
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7
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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
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10
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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
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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
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1
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2.3k
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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
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13
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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
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6
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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
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1
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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
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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
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10
replies
6.8k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.8 years ago Robert ▴ 10
0
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2
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2.5k
views
GenomicRanges error constructing Granges
granges
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
2
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1
reply
886
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
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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
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3
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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
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2
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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
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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
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1
reply
924
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
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1
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771
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
5.4 years ago Shaurya Jauhari • 0
1
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2
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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
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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
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1
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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
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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
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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
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8
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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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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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