Showing : granges • reset
0
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2
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147
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
17 days ago • updated 14 days ago Arslan • 0
0
votes
5
replies
219
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
12 weeks ago rtrivedi1 ▴ 10
0
votes
1
reply
170
views
annotateWithGeneParts
GRanges
updated 4 months ago by ★ 1.5k • written 4 months ago by • 0
1
vote
2
replies
217
views
Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges ORFik openreadingframe circulargenome findORFsFasta
updated 6 months ago by ▴ 80 • written 6 months ago by • 0
11
votes
17
replies
12k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 6.9 years ago by ▴ 120
1
vote
3
replies
261
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
10 months ago rahnaman ▴ 10
0
votes
4
replies
268
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Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 11 months ago by 58k • written 11 months ago by ▴ 20
0
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1
reply
190
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 11 months ago by ▴ 130 • written 16 months ago by • 0
6
votes
3
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272
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How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 12 months ago by ▴ 30 • written 12 months ago by ▴ 10
3
votes
7
replies
375
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 13 months ago by 58k • written 13 months ago by ▴ 10
8
votes
10
replies
391
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 15 months ago by 58k • written 15 months ago by ▴ 50
2
votes
2
replies
250
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 16 months ago by 15k • written 16 months ago by ▴ 10
1
vote
1
reply
348
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 17 months ago by 11k • written 17 months ago by ▴ 20
7
votes
13
replies
659
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 18 months ago by ★ 2.7k • written 18 months ago by ▴ 90
0
votes
6
replies
303
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 19 months ago by 43k • written 19 months ago by ▴ 20
0
votes
1
reply
293
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 22 months ago by 15k • written 22 months ago by • 0
3
votes
12
replies
530
views
Understanding group_by, reduce_ranges,
plyranges granges
updated 22 months ago by ▴ 70 • written 22 months ago by ▴ 70
4
votes
9
replies
441
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 2.0 years ago by 58k • written 2.0 years ago by • 0
7
votes
8
replies
5.3k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 2.2 years ago by ▴ 40 • written 5.9 years ago by ▴ 50
3
votes
10
replies
2.0k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
2.2 years ago Robert ▴ 10
4
votes
2
replies
499
views
Build GPos from IPos
genomicranges granges gpos
updated 2.3 years ago by 15k • written 3.0 years ago by ▴ 140
0
votes
2
replies
1.0k
views
GenomicRanges error constructing Granges
granges
updated 2.5 years ago by 58k • written 2.5 years ago by • 0
2
votes
1
reply
332
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 2.5 years ago by 58k • written 2.5 years ago by ▴ 40
4
votes
1
reply
373
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 2.5 years ago by 11k • written 2.5 years ago by ▴ 140
1
vote
3
replies
418
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 2.5 years ago by 15k • written 2.6 years ago by • 0
2
votes
1
reply
672
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 2.6 years ago by 58k • written 2.6 years ago by ▴ 40
3
votes
2
replies
651
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 2.6 years ago by ★ 1.9k • written 2.6 years ago by ▴ 80
5
votes
8
replies
1.0k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 2.6 years ago by 25k • written 2.6 years ago by ▴ 70
0
votes
4
replies
468
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 2.6 years ago by 58k • written 2.6 years ago by • 0
6
votes
12
replies
637
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
2.6 years ago foehn ▴ 80
0
votes
1
reply
338
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 2.7 years ago by 58k • written 2.7 years ago by • 0
2
votes
4
replies
518
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 2.8 years ago by 58k • written 2.8 years ago by ▴ 10
0
votes
1
reply
366
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
2.8 years ago Shaurya Jauhari • 0
4
votes
7
replies
5.4k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.8 years ago by ▴ 10 • written 6.0 years ago by ▴ 50
1
vote
2
replies
432
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
2.8 years ago Arman Shahrisa ▴ 20
2
votes
4
replies
496
views
Split GRanges to GRangeList based on mcols value
granges
updated 2.9 years ago by 11k • written 2.9 years ago by ▴ 10
1
vote
2
replies
519
views
Split AME .tsv file into GRanges object or DataFrame
meme ame motif dataframe granges
updated 2.9 years ago by 11k • written 2.9 years ago by ▴ 60
2
votes
1
reply
454
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 3.0 years ago by 15k • written 3.0 years ago by ▴ 140
0
votes
3
replies
819
views
Selecting columns form a list of grange objects
r granges grange
3.0 years ago g.k • 0
2
votes
2
replies
1.7k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 3.0 years ago by 58k • written 3.0 years ago by • 0
4
votes
8
replies
576
views
the closest gene to a breakpoint
granges plyranges
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 620
0
votes
1
reply
821
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
3.1 years ago jerrywu1987 • 0
5
votes
9
replies
1.1k
views
subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 3.1 years ago by ▴ 70 • written 3.1 years ago by ▴ 620
1
vote
1
reply
381
views
Subsetting GRanges objext
GRanges subsetting
updated 3.1 years ago by 58k • written 3.1 years ago by • 0
0
votes
7
replies
826
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.2 years ago by • 0 • written 3.2 years ago by • 0
2
votes
1
reply
569
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 40
0
votes
4
replies
730
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
0
votes
1
reply
514
views
Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
3.5 years ago g.k • 0
0
votes
0
replies
430
views
Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
3.5 years ago A ▴ 40
1
vote
2
replies
580
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 3.5 years ago by 11k • written 3.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Comment: "full model matrix is less than full rank" by fernandogs97 • 0
Hello ATpoint, thank you very much for your fast and helpful response, finally I corrected the error by changing the separator, instead of …
Comment: unable to load shared object Rsamtools.dll': by Mike Smith ★ 5.1k
Can you include the command you're running (I guess it's `BiocManager::install("Rsamtools", type = "source")` )? It would also be useful to…
Comment: unable to load shared object Rsamtools.dll': by franck.richard • 0
Finally, I only encounter this problem with Rsamtools. It works fine with the other packages. Thank you for your help!
Comment: Unique GPos taking into account mcols by maltethodberg ▴ 140
Yes, I managed to find those functions via the VariantAnnotation package. The "Quad" versions are very handy for matching seqnames/pos/effe…
Votes
Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
Comment: deseq2 machine sizing best practices for very large data set
Comment: Warning messages on Apple M1 BigSur
Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset
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