Showing : granges • reset
0
votes
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85
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annotateWithGeneParts
GRanges
updated 28 days ago by ★ 1.5k • written 29 days ago by • 0
1
vote
2
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152
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Error when using ORFik: findORFsFasta gives wrong start and stop codon
GRanges ORFik openreadingframe circulargenome findORFsFasta
updated 3 months ago by ▴ 80 • written 3 months ago by • 0
11
votes
17
replies
12k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 6.7 years ago by ▴ 120
1
vote
3
replies
191
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
7 months ago rahnaman ▴ 10
0
votes
4
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200
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 8 months ago by 57k • written 8 months ago by ▴ 20
0
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1
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136
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need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR granges iranges
updated 8 months ago by ▴ 130 • written 13 months ago by • 0
6
votes
3
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215
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 9 months ago by ▴ 30 • written 9 months ago by ▴ 10
3
votes
7
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287
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 10 months ago by 57k • written 10 months ago by ▴ 10
8
votes
10
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297
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 12 months ago by 57k • written 12 months ago by ▴ 50
2
votes
2
replies
165
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 13 months ago by 15k • written 13 months ago by ▴ 10
1
vote
1
reply
244
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 14 months ago by 11k • written 14 months ago by ▴ 20
7
votes
13
replies
512
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 15 months ago by ★ 2.7k • written 15 months ago by ▴ 90
0
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6
replies
214
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 16 months ago by 43k • written 16 months ago by ▴ 20
0
votes
1
reply
233
views
Calculating and plotting AT content in a tiling window across the genome with GRanges
bioconductor biostrings gc content biostring granges
updated 19 months ago by 15k • written 19 months ago by • 0
3
votes
12
replies
406
views
Understanding group_by, reduce_ranges,
plyranges granges
updated 19 months ago by ▴ 70 • written 19 months ago by ▴ 60
4
votes
9
replies
346
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 21 months ago by 57k • written 21 months ago by • 0
7
votes
8
replies
5.0k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 23 months ago by ▴ 40 • written 5.7 years ago by ▴ 50
3
votes
10
replies
1.7k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
23 months ago Robert ▴ 10
4
votes
2
replies
435
views
Build GPos from IPos
genomicranges granges gpos
updated 2.0 years ago by 15k • written 2.7 years ago by ▴ 140
0
votes
2
replies
882
views
GenomicRanges error constructing Granges
granges
updated 2.2 years ago by 57k • written 2.2 years ago by • 0
2
votes
1
reply
289
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 2.3 years ago by 57k • written 2.3 years ago by ▴ 40
4
votes
1
reply
328
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 2.3 years ago by 11k • written 2.3 years ago by ▴ 140
1
vote
3
replies
370
views
Obtain coordinates of 5' upstream region up to closest coding region
r granges promoter
updated 2.3 years ago by 15k • written 2.3 years ago by • 0
2
votes
1
reply
613
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 2.3 years ago by 57k • written 2.3 years ago by ▴ 40
3
votes
2
replies
568
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by ▴ 60
5
votes
8
replies
911
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 2.4 years ago by 25k • written 2.4 years ago by ▴ 60
0
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4
replies
399
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 2.4 years ago by 57k • written 2.4 years ago by • 0
3
votes
12
replies
503
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
2.4 years ago foehn ▴ 60
0
votes
1
reply
305
views
Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 2.4 years ago by 57k • written 2.4 years ago by • 0
2
votes
4
replies
464
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 2.5 years ago by 57k • written 2.5 years ago by ▴ 10
0
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1
reply
323
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
2.5 years ago Shaurya Jauhari • 0
3
votes
7
replies
5.1k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.5 years ago by • 0 • written 5.7 years ago by ▴ 50
1
vote
2
replies
382
views
Obtain GRanges object by gene names
GRanges gene symbol IdeoViz
2.6 years ago Arman Shahrisa ▴ 20
2
votes
4
replies
412
views
Split GRanges to GRangeList based on mcols value
granges
updated 2.6 years ago by 11k • written 2.6 years ago by ▴ 10
1
vote
2
replies
457
views
Split AME .tsv file into GRanges object or DataFrame
meme ame motif dataframe granges
updated 2.6 years ago by 11k • written 2.6 years ago by ▴ 60
2
votes
1
reply
406
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 2.7 years ago by 15k • written 2.7 years ago by ▴ 140
0
votes
3
replies
699
views
Selecting columns form a list of grange objects
r granges grange
2.7 years ago g.k • 0
2
votes
2
replies
1.5k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 2.8 years ago by 57k • written 2.8 years ago by • 0
4
votes
8
replies
515
views
the closest gene to a breakpoint
granges plyranges
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 610
0
votes
1
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753
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
2.8 years ago jerrywu1987 • 0
5
votes
9
replies
689
views
subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 2.8 years ago by ▴ 70 • written 2.8 years ago by ▴ 610
1
vote
1
reply
342
views
Subsetting GRanges objext
GRanges subsetting
updated 2.8 years ago by 57k • written 2.8 years ago by • 0
0
votes
7
replies
726
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
2
votes
1
reply
500
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 3.0 years ago by ★ 26k • written 3.0 years ago by ▴ 40
0
votes
4
replies
657
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.0 years ago by 57k • written 3.0 years ago by • 0
0
votes
1
reply
425
views
Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
3.2 years ago g.k • 0
0
votes
0
replies
392
views
Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
3.2 years ago A ▴ 40
1
vote
2
replies
529
views
Detecting Overlaps within Grange Object
r grange granges iranges
updated 3.2 years ago by 11k • written 3.2 years ago by • 0
0
votes
1
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397
views
R_Granges_adding merged Metadata columns
granges findoverlaps
3.2 years ago me.saichi • 0
2
votes
2
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483
views
Features within 2kb window, but with resampling
genomicranges granges slidingwindow
updated 3.2 years ago by 11k • written 3.2 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: lmFit, number of proteins by AyHi • 0
Dear Gordnon, Thank you, your reply was very helpful!
Comment: Salmon, RUVSeq and DESeq2 by reganhayward • 0
Legend - thanks Mike
Comment: Salmon, RUVSeq and DESeq2 by Michael Love 33k
The SVA workflow doesn't have any steps to account for sequencing depth, hence we recommend supplying the scaled counts to SVA. However, R…
Comment: Issues with Tximport by bryce.thomas • 0
While this line of code did fix the dataframe called by `tx2gene` it still has issues. However, if you toggle `txOut = FALSE` to `txOut = T…
Comment: how to plot multiple RLEs on same plot? by xiaofeiwang18266 ▴ 20
@James W. MacDonald Thank you so much for your time and answer! It is much more condensed by adjusting the margin. But, I remembered it sh…
Votes
Answer: lmFit, number of proteins
Answer: lmFit, number of proteins
C: clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplo
C: clusterProfiler - GeneRatio & nb of genes always positively correlated in dotplo
Answer: edgeR calcNormFactors or normalize with voom?
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