Showing : granges • reset
0
votes
2
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153
views
cannot install various functions in R
GRanges packages installation
updated 11 days ago by 3.1k • written 11 days ago by • 0
1
vote
2
replies
265
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 7 months ago by ★ 5.5k • written 7 months ago by ★ 1.5k
0
votes
2
replies
329
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
8 months ago Arslan • 0
0
votes
5
replies
385
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
10 months ago rtrivedi1 ▴ 10
0
votes
1
reply
395
views
annotateWithGeneParts
GRanges
updated 11 months ago by ★ 1.6k • written 11 months ago by • 0
1
vote
2
replies
404
views
Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges ORFik openreadingframe circulargenome findORFsFasta
updated 14 months ago by ▴ 80 • written 14 months ago by • 0
12
votes
19
replies
14k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 3 months ago by ▴ 30 • written 7.6 years ago by ▴ 120
1
vote
3
replies
369
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
18 months ago rahnaman ▴ 10
0
votes
4
replies
408
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 19 months ago by 59k • written 19 months ago by ▴ 20
0
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1
reply
289
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 19 months ago by ▴ 140 • written 2.0 years ago by • 0
6
votes
3
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589
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 20 months ago by ▴ 60 • written 20 months ago by ▴ 10
3
votes
7
replies
713
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 21 months ago by 59k • written 21 months ago by ▴ 10
8
votes
10
replies
543
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 23 months ago by 59k • written 23 months ago by ▴ 50
2
votes
2
replies
425
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 24 months ago by 15k • written 24 months ago by ▴ 10
1
vote
1
reply
712
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 20
7
votes
13
replies
1.0k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 2.2 years ago by ★ 2.8k • written 2.2 years ago by ▴ 90
0
votes
6
replies
513
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 2.2 years ago by 45k • written 2.2 years ago by ▴ 20
0
votes
1
reply
444
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 2.5 years ago by 15k • written 2.5 years ago by • 0
3
votes
12
replies
750
views
Understanding group_by, reduce_ranges,
plyranges granges
updated 2.5 years ago by ▴ 70 • written 2.5 years ago by ▴ 70
4
votes
9
replies
683
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 2.7 years ago by 59k • written 2.7 years ago by • 0
7
votes
8
replies
5.9k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 2.8 years ago by ▴ 40 • written 6.6 years ago by ▴ 50
3
votes
10
replies
3.1k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
2.9 years ago • updated 2.8 years ago Robert ▴ 10
4
votes
2
replies
618
views
Build GPos from IPos
genomicranges granges gpos
updated 2.9 years ago by 15k • written 3.6 years ago by ▴ 140
0
votes
2
replies
1.3k
views
GenomicRanges error constructing Granges
granges
updated 3.1 years ago by 59k • written 3.1 years ago by • 0
2
votes
1
reply
419
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 3.2 years ago by 59k • written 3.2 years ago by ▴ 40
4
votes
1
reply
498
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 3.2 years ago by 11k • written 3.2 years ago by ▴ 140
1
vote
3
replies
550
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 3.2 years ago by 15k • written 3.2 years ago by • 0
2
votes
1
reply
857
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 3.2 years ago by 59k • written 3.2 years ago by ▴ 40
3
votes
2
replies
862
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 3.2 years ago by ★ 1.9k • written 3.2 years ago by ▴ 80
5
votes
8
replies
1.3k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 3.3 years ago by 25k • written 3.3 years ago by ▴ 70
0
votes
4
replies
561
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 3.3 years ago by 59k • written 3.3 years ago by • 0
6
votes
12
replies
857
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
3.3 years ago foehn ▴ 80
0
votes
1
reply
404
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 3.3 years ago by 59k • written 3.3 years ago by • 0
2
votes
4
replies
656
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 3.4 years ago by 59k • written 3.4 years ago by ▴ 10
0
votes
1
reply
440
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
3.4 years ago Shaurya Jauhari • 0
5
votes
8
replies
6.2k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3 months ago by • 0 • written 6.6 years ago by ▴ 50
1
vote
2
replies
534
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
3.5 years ago Arman Shahrisa ▴ 20
2
votes
4
replies
633
views
Split GRanges to GRangeList based on mcols value
granges
updated 3.5 years ago by 11k • written 3.5 years ago by ▴ 10
1
vote
2
replies
663
views
Split AME .tsv file into GRanges object or DataFrame
meme ame motif dataframe granges
updated 3.5 years ago by 11k • written 3.5 years ago by ▴ 60
2
votes
1
reply
562
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 3.6 years ago by 15k • written 3.6 years ago by ▴ 140
0
votes
3
replies
1.1k
views
Selecting columns form a list of grange objects
r granges grange
3.6 years ago g.k • 0
2
votes
2
replies
2.1k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 3.7 years ago by 59k • written 3.7 years ago by • 0
4
votes
8
replies
678
views
the closest gene to a breakpoint
granges plyranges
updated 3.7 years ago by 45k • written 3.7 years ago by ▴ 640
0
votes
1
reply
1.0k
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
3.7 years ago jerrywu1987 • 0
5
votes
9
replies
2.8k
views
subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 3.7 years ago by ▴ 70 • written 3.7 years ago by ▴ 640
1
vote
1
reply
467
views
Subsetting GRanges objext
GRanges subsetting
updated 3.7 years ago by 59k • written 3.7 years ago by • 0
0
votes
7
replies
1.1k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
2
votes
1
reply
732
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 3.9 years ago by ★ 27k • written 3.9 years ago by ▴ 40
0
votes
4
replies
940
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.9 years ago by 59k • written 3.9 years ago by • 0
0
votes
1
reply
580
views
Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
4.1 years ago g.k • 0
50 results • Page 1 of 1
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Comment: EnrichGO not working with db created from annotationhub by Guido Hooiveld ★ 3.2k
Part 2; continuation of Part 1 above... > # !! got same error as reported !! > > # ... but do these 150 LOCs have a GO annotat…
Comment: EnrichGO not working with db created from annotationhub by Guido Hooiveld ★ 3.2k
I had a closer look at this, and the error you got is actually somewhat misleading; it is not that you are using the wrong ids (ids that ar…
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld by vanbelj ▴ 10
Below is a [solution][1] to extract and average counts across replicates from a dds using Base R. If you're familiar with ```limma``` you …
Comment: featureCounts: 0% successfully assigned fragments by KMS • 0
Sorry for the incomplete information. I have bacterial RNASeq pair end data and using subread/Rsubread on Rstudio and ubuntu, after few sec…
Comment: Variance explained (coefficient of determination) in edgeR by Gordon Smyth 45k
No, you have it wrong way around. If you want deviance explained by x1, then you need ``` R2_x1 <- ( deviance without x1 in model - devia…
Votes
Comment: cellCounts() function floating point error
Comment: cellCounts() function floating point error
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
Answer: Use MulticoreParam under BatchtoolsParam
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