Showing : granges • reset
0
votes
1
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227
views
GRanges list convert into igraph format
GRanges igraph
updated 4 months ago by ▴ 710 • written 4 months ago by ▴ 660
3
votes
1
reply
306
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 5 months ago by 40k • written 5 months ago by • 0
2
votes
1
reply
752
views
Removing metadata rows containing NA values in GRanges
IRanges GRanges NA
updated 8 months ago by ★ 2.9k • written 8 months ago by • 0
2
votes
5
replies
544
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
9 months ago Marcus • 0
1
vote
1
reply
443
views
lapply for GRanges
lapply GRanges
updated 12 months ago by 16k • written 12 months ago by • 0
2
votes
2
replies
1.8k
views
Feature request: syntax for dropping unused seqlevels in GRanges objects
granges seqlevels feature request
updated 12 months ago by ▴ 20 • written 6.1 years ago by ▴ 170
0
votes
2
replies
596
views
cannot install various functions in R
GRanges packages installation
updated 13 months ago by 3.5k • written 13 months ago by • 0
1
vote
2
replies
546
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 20 months ago by ★ 6.0k • written 20 months ago by ★ 1.5k
0
votes
2
replies
644
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
21 months ago Arslan • 0
0
votes
5
replies
1.2k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
23 months ago rtrivedi1 ▴ 10
0
votes
1
reply
845
views
annotateWithGeneParts
GRanges
updated 2.0 years ago by ★ 1.6k • written 2.0 years ago by • 0
1
vote
2
replies
678
views
Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges ORFik openreadingframe circulargenome findORFsFasta
updated 2.2 years ago by ▴ 80 • written 2.2 years ago by • 0
14
votes
19
replies
17k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 16 months ago by ▴ 50 • written 8.6 years ago by ▴ 120
1
vote
3
replies
943
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
2.5 years ago rahnaman ▴ 10
0
votes
4
replies
745
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 2.6 years ago by 63k • written 2.6 years ago by ▴ 20
0
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1
reply
546
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 2.6 years ago by ▴ 150 • written 3.0 years ago by • 0
6
votes
3
replies
2.0k
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 2.8 years ago by ▴ 60 • written 2.8 years ago by ▴ 10
3
votes
7
replies
1.0k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 2.8 years ago by 63k • written 2.8 years ago by ▴ 20
8
votes
10
replies
1.1k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 3.0 years ago by 63k • written 3.0 years ago by ▴ 50
2
votes
2
replies
780
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 10
1
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1
reply
1.4k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 3.2 years ago by 11k • written 3.2 years ago by ▴ 20
7
votes
13
replies
1.7k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 3.2 years ago by ★ 3.0k • written 3.2 years ago by ▴ 110
0
votes
6
replies
1.1k
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 3.3 years ago by 47k • written 3.3 years ago by ▴ 20
0
votes
1
reply
715
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
3
votes
12
replies
1.3k
views
Understanding group_by, reduce_ranges,
plyranges granges
updated 3.6 years ago by ▴ 70 • written 3.6 years ago by ▴ 80
4
votes
9
replies
1.1k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 3.7 years ago by 63k • written 3.7 years ago by • 0
8
votes
8
replies
7.1k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 3.9 years ago by ▴ 40 • written 7.6 years ago by ▴ 50
3
votes
10
replies
5.0k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
3.9 years ago Robert ▴ 10
4
votes
2
replies
836
views
Build GPos from IPos
genomicranges granges gpos
updated 3.9 years ago by 16k • written 4.7 years ago by ▴ 160
0
votes
2
replies
1.8k
views
GenomicRanges error constructing Granges
granges
updated 4.2 years ago by 63k • written 4.2 years ago by • 0
2
votes
1
reply
621
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 4.2 years ago by 63k • written 4.2 years ago by ▴ 40
4
votes
1
reply
786
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 4.2 years ago by 11k • written 4.2 years ago by ▴ 160
1
vote
3
replies
875
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 4.2 years ago by 16k • written 4.3 years ago by • 0
2
votes
1
reply
1.1k
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 4.3 years ago by 63k • written 4.3 years ago by ▴ 40
3
votes
2
replies
1.2k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 4.3 years ago by ★ 2.0k • written 4.3 years ago by ▴ 80
6
votes
8
replies
2.0k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 4.3 years ago by 25k • written 4.3 years ago by ▴ 80
0
votes
4
replies
773
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 4.3 years ago by 63k • written 4.3 years ago by • 0
6
votes
12
replies
1.3k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
4.3 years ago foehn ▴ 80
0
votes
1
reply
637
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 4.4 years ago by 63k • written 4.4 years ago by • 0
2
votes
4
replies
983
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 4.5 years ago by 63k • written 4.5 years ago by ▴ 10
0
votes
1
reply
564
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
4.5 years ago Shaurya Jauhari • 0
5
votes
8
replies
7.5k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 15 months ago by • 0 • written 7.7 years ago by ▴ 50
1
vote
2
replies
722
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
4.5 years ago Arman Shahrisa ▴ 20
2
votes
4
replies
891
views
Split GRanges to GRangeList based on mcols value
granges
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 10
1
vote
2
replies
903
views
Split AME .tsv file into GRanges object or DataFrame
meme ame motif dataframe granges
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 60
2
votes
1
reply
742
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 160
0
votes
3
replies
1.7k
views
Selecting columns form a list of grange objects
r granges grange
4.7 years ago g.k • 0
2
votes
2
replies
3.0k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 4.7 years ago by 63k • written 4.7 years ago by • 0
4
votes
8
replies
987
views
the closest gene to a breakpoint
granges plyranges
updated 4.8 years ago by 47k • written 4.8 years ago by ▴ 660
0
votes
1
reply
1.3k
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
4.8 years ago jerrywu1987 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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