Showing : GRanges • reset
0
votes
1
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483
views
GRanges list convert into igraph format
GRanges igraph
updated 10 months ago by ▴ 720 • written 10 months ago by ▴ 670
3
votes
1
reply
538
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 11 months ago by 41k • written 11 months ago by • 0
2
votes
1
reply
1.3k
views
Removing metadata rows containing NA values in GRanges
IRanges GRanges NA
updated 14 months ago by ★ 3.6k • written 14 months ago by • 0
2
votes
5
replies
1.0k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
15 months ago Marcus • 0
1
vote
1
reply
688
views
lapply for GRanges
lapply GRanges
updated 18 months ago by 16k • written 18 months ago by • 0
2
votes
2
replies
2.1k
views
Feature request: syntax for dropping unused seqlevels in GRanges objects
granges seqlevels feature request
updated 18 months ago by ▴ 20 • written 6.6 years ago by ▴ 180
0
votes
2
replies
837
views
cannot install various functions in R
GRanges packages installation
updated 19 months ago by 3.6k • written 19 months ago by • 0
1
vote
2
replies
776
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 2.2 years ago by ★ 6.2k • written 2.2 years ago by ★ 1.5k
0
votes
2
replies
861
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.2 years ago Arslan • 0
0
votes
5
replies
1.9k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.4 years ago rtrivedi1 ▴ 10
0
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1
reply
1.1k
views
annotateWithGeneParts
GRanges
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
1
vote
2
replies
837
views
Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges ORFik openreadingframe circulargenome findORFsFasta
updated 2.7 years ago by ▴ 80 • written 2.7 years ago by • 0
14
votes
19
replies
18k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 22 months ago by ▴ 60 • written 9.1 years ago by ▴ 120
1
vote
3
replies
1.4k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
3.0 years ago rahnaman ▴ 10
0
votes
4
replies
985
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 3.1 years ago by 64k • written 3.1 years ago by ▴ 20
0
votes
1
reply
729
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 3.1 years ago by ▴ 150 • written 3.5 years ago by • 0
6
votes
3
replies
3.0k
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 3.2 years ago by ▴ 100 • written 3.3 years ago by ▴ 10
3
votes
7
replies
1.3k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.3 years ago by 64k • written 3.3 years ago by ▴ 20
8
votes
10
replies
1.6k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 3.5 years ago by 64k • written 3.5 years ago by ▴ 50
2
votes
2
replies
1.0k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.5 years ago by 16k • written 3.5 years ago by ▴ 10
1
vote
1
reply
1.9k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 3.6 years ago by 11k • written 3.6 years ago by ▴ 20
7
votes
13
replies
2.2k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 3.7 years ago by ★ 3.0k • written 3.7 years ago by ▴ 110
0
votes
6
replies
1.6k
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 3.8 years ago by 48k • written 3.8 years ago by ▴ 20
0
votes
1
reply
898
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 4.1 years ago by 16k • written 4.1 years ago by • 0
3
votes
12
replies
1.7k
views
Understanding group_by, reduce_ranges,
plyranges granges
updated 4.1 years ago by ▴ 70 • written 4.1 years ago by ▴ 80
4
votes
9
replies
1.4k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 4.2 years ago by 64k • written 4.2 years ago by • 0
8
votes
8
replies
7.6k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 4.3 years ago by ▴ 40 • written 8.1 years ago by ▴ 50
3
votes
10
replies
6.0k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
4.4 years ago Robert ▴ 10
4
votes
2
replies
969
views
Build GPos from IPos
genomicranges granges gpos
updated 4.4 years ago by 16k • written 5.2 years ago by ▴ 170
0
votes
2
replies
2.2k
views
GenomicRanges error constructing Granges
granges
updated 4.7 years ago by 64k • written 4.7 years ago by • 0
2
votes
1
reply
767
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 4.7 years ago by 64k • written 4.7 years ago by ▴ 40
4
votes
1
reply
942
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 170
1
vote
3
replies
1.1k
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 4.7 years ago by 16k • written 4.7 years ago by • 0
2
votes
1
reply
1.2k
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 4.8 years ago by 64k • written 4.8 years ago by ▴ 40
3
votes
2
replies
1.5k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 4.8 years ago by ★ 2.0k • written 4.8 years ago by ▴ 100
6
votes
8
replies
2.4k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 4.8 years ago by 25k • written 4.8 years ago by ▴ 80
0
votes
4
replies
973
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 4.8 years ago by 64k • written 4.8 years ago by • 0
6
votes
12
replies
1.6k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
4.8 years ago foehn ▴ 100
0
votes
1
reply
795
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 4.9 years ago by 64k • written 4.9 years ago by • 0
2
votes
4
replies
1.2k
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 5.0 years ago by 64k • written 5.0 years ago by ▴ 10
0
votes
1
reply
662
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
5.0 years ago Shaurya Jauhari • 0
5
votes
8
replies
8.2k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 21 months ago by • 0 • written 8.2 years ago by ▴ 50
1
vote
2
replies
830
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
5.0 years ago Arman Shahrisa ▴ 20
2
votes
4
replies
1.1k
views
Split GRanges to GRangeList based on mcols value
granges
updated 5.0 years ago by 11k • written 5.0 years ago by ▴ 10
1
vote
2
replies
1.0k
views
Split AME .tsv file into GRanges object or DataFrame
meme ame motif dataframe granges
updated 5.1 years ago by 11k • written 5.1 years ago by ▴ 60
2
votes
1
reply
864
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 5.2 years ago by 16k • written 5.2 years ago by ▴ 170
0
votes
3
replies
2.0k
views
Selecting columns form a list of grange objects
r granges grange
5.2 years ago g.k • 0
2
votes
2
replies
3.5k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 5.2 years ago by 64k • written 5.2 years ago by • 0
4
votes
8
replies
1.3k
views
the closest gene to a breakpoint
granges plyranges
updated 5.3 years ago by 48k • written 5.3 years ago by ▴ 670
0
votes
1
reply
1.5k
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
5.3 years ago jerrywu1987 • 0
50 results • Page 1 of 1
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Comment: Why is DMRcate not available for Bioconductor version 3.18? by Daniel E. Weeks ▴ 20
Thank you for the explanation and contacting the DSS package authors.
Comment: Why is DMRcate not available for Bioconductor version 3.18? by shepherl 3.6k
The DSS package authors just need to add `edgeR` to their Suggest of their DESCRIPTION. They have been contacted about it but have not acte…
Answer: GOslim missing GO term by James W. MacDonald 64k
I think it's because that GO term isn't an offspring of any term in the GO slim you are downloading. ``` > ids<- "GO:0002831" > slim <…
Answer: Obtaining rsIDs with ENSG and variant ID information by Robert Castelo ★ 3.0k
You should first and foremost find out what was the human reference genome version from which your dataset was derived. Assuming this was G…
Comment: DESeq2 - groups with biological replicates from the same patient by James W. MacDonald 64k
If by clustering you mean there might be a within-subject correlation, then yes it's a possibility. But you cannot control for that using a…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
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