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Showing :
granges
•
reset
0
votes
2
replies
153
views
cannot install various functions in R
GRanges
packages
installation
updated 11 days ago by
shepherl
3.1k • written 11 days ago by
Eli
• 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
Mike Smith
★ 5.5k • written 7 months ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
329
views
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
Malcolm Cook
★ 1.6k • written 11 months ago by
Punjika
• 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
hauken_heyken
▴ 80 • written 14 months ago by
levasseurmaxence
• 0
12
votes
19
replies
14k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 3 months ago by
Nadine
▴ 30 • written 7.6 years ago by
Darya Vanichkina
▴ 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
James W. MacDonald
59k • written 19 months ago by
biomiha
▴ 20
0
votes
1
reply
289
views
need help with overlap overrepresentation using permutation tests for composite genomic ranges
regioneR
granges
iranges
updated 19 months ago by
bernatgel
▴ 140 • written 2.0 years ago by
Angel Liang
• 0
6
votes
3
replies
589
views
How do I subset a GRanges object based on chromosome (and approximate region)?
GRanges
updated 20 months ago by
merv
▴ 60 • written 20 months ago by
deepue
▴ 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
James W. MacDonald
59k • written 21 months ago by
vanbelj
▴ 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
James W. MacDonald
59k • written 23 months ago by
omarrafiqued
▴ 50
2
votes
2
replies
425
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 24 months ago by
Hervé Pagès
15k • written 24 months ago by
Robert
▴ 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
Michael Lawrence
11k • written 2.1 years ago by
ssabri
▴ 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
Robert Castelo
★ 2.8k • written 2.2 years ago by
Biologist
▴ 90
0
votes
6
replies
513
views
GenomicRanges: Find first, second and third nearest genes
R
GenomicRanges
Granges
updated 2.2 years ago by
Gordon Smyth
45k • written 2.2 years ago by
ssabri
▴ 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
Hervé Pagès
15k • written 2.5 years ago by
atotalamateur
• 0
3
votes
12
replies
750
views
Understanding group_by, reduce_ranges,
plyranges
granges
updated 2.5 years ago by
lee.s
▴ 70 • written 2.5 years ago by
Konstantinos Yeles
▴ 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
James W. MacDonald
59k • written 2.7 years ago by
new_user6
• 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
balwierz
▴ 40 • written 6.6 years ago by
vinod.acear
▴ 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
Hervé Pagès
15k • written 3.6 years ago by
maltethodberg
▴ 140
0
votes
2
replies
1.3k
views
GenomicRanges error constructing Granges
granges
updated 3.1 years ago by
James W. MacDonald
59k • written 3.1 years ago by
rhooads7
• 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
James W. MacDonald
59k • written 3.2 years ago by
jacorvar
▴ 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
Michael Lawrence
11k • written 3.2 years ago by
maltethodberg
▴ 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
Hervé Pagès
15k • written 3.2 years ago by
eggrandio
• 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
James W. MacDonald
59k • written 3.2 years ago by
Vinicius Henrique da Silva
▴ 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
Johannes Rainer
★ 1.9k • written 3.2 years ago by
foehn
▴ 80
5
votes
8
replies
1.3k
views
Ranges from a fasta file
biostrings
fasta
genomicranges
granges
updated 3.3 years ago by
Martin Morgan
25k • written 3.3 years ago by
Konstantinos Yeles
▴ 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
James W. MacDonald
59k • written 3.3 years ago by
ferbecneu
• 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
James W. MacDonald
59k • written 3.3 years ago by
lalchungnungabt17
• 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
James W. MacDonald
59k • written 3.4 years ago by
olavur
▴ 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
b.simpson
• 0 • written 6.6 years ago by
vinod.acear
▴ 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
Michael Lawrence
11k • written 3.5 years ago by
unamourdeswann
▴ 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
Michael Lawrence
11k • written 3.5 years ago by
rbronste
▴ 60
2
votes
1
reply
562
views
Intra-range transformation on GPos-objects?
genomicranges
gpos
granges
updated 3.6 years ago by
Hervé Pagès
15k • written 3.6 years ago by
maltethodberg
▴ 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
James W. MacDonald
59k • written 3.7 years ago by
g.k
• 0
4
votes
8
replies
678
views
the closest gene to a breakpoint
granges
plyranges
updated 3.7 years ago by
Gordon Smyth
45k • written 3.7 years ago by
Bogdan
▴ 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
lee.s
▴ 70 • written 3.7 years ago by
Bogdan
▴ 640
1
vote
1
reply
467
views
Subsetting GRanges objext
GRanges
subsetting
updated 3.7 years ago by
James W. MacDonald
59k • written 3.7 years ago by
lalchungnungabt17
• 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
spotifywebplayer
• 0 • written 3.8 years ago by
jinseok
• 0
2
votes
1
reply
732
views
Error to rename seqlevels in Granges interactions
interactionset
granges
updated 3.9 years ago by
Aaron Lun
★ 27k • written 3.9 years ago by
Vinicius Henrique da Silva
▴ 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
James W. MacDonald
59k • written 3.9 years ago by
q.thomas
• 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
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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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