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Showing :
GenomicRanges
•
reset
0
votes
0
replies
115
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
5 weeks ago
gshweta95
• 0
0
votes
0
replies
198
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
10 weeks ago
mat149
▴ 70
2
votes
1
reply
262
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
12 weeks ago
mat149
▴ 70
0
votes
2
replies
770
views
GenomicRanges coult not be loaded after R upgrade
DESeq2
Bioconductor
GenomicRanges
updated 12 months ago by
Virginie
• 0 • written 12 months ago by
gs12
• 0
3
votes
4
replies
929
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges
IRanges
updated 13 months ago by
Hervé Pagès
16k • written 13 months ago by
jbendik
• 0
0
votes
1
reply
617
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
589
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
15 months ago
Delta._.43
▴ 20
4
votes
4
replies
1.2k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Dario Strbenac
★ 1.5k
3
votes
1
reply
708
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges
GenomicRanges
updated 16 months ago by
Michael Love
41k • written 16 months ago by
d.s.h.andel-3
• 0
0
votes
2
replies
1.1k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 17 months ago by
Malcolm Cook
★ 1.6k • written 18 months ago by
mike-zx
• 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
19 months ago
Mog
• 0
0
votes
0
replies
569
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago
Simon Coetzee
▴ 50
2
votes
3
replies
1.7k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges
plyranges
22 months ago
Rodrigo
• 0
0
votes
1
reply
961
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 22 months ago by
James W. MacDonald
65k • written 22 months ago by
Johanna
• 0
3
votes
2
replies
1.3k
views
toGRanges help!
GenomicRanges
toGRanges
Bioconductor
23 months ago
samantha.haque
• 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
2.0 years ago
vanbelj
▴ 30
0
votes
1
reply
970
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
779
views
How about a getSeq() method for GRanges ?
GenomicRanges
BSGenome
2.1 years ago
Charles Plessy
▴ 180
0
votes
2
replies
3.7k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 2.1 years ago by
kent.riemondy
▴ 20 • written 2.1 years ago by
svenbioinf
• 0
0
votes
6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges
methylKit
S4Vectors
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
hasche
• 0
0
votes
0
replies
687
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation
CNVRanger
GenomicRanges
2.2 years ago
svlachavas
▴ 830
6
votes
2
replies
1.2k
views
strand-aware GRanges shift
GenomicRanges
updated 2.2 years ago by
Malcolm Cook
★ 1.6k • written 2.2 years ago by
gene_bioconductor
▴ 10
9
votes
9
replies
3.2k
views
Subset GRanges by intersection
findOverlaps
GPos
GenomicRanges
subsetByOverlaps
updated 2.3 years ago by
James W. MacDonald
65k • written 2.3 years ago by
Robert
▴ 10
3
votes
5
replies
1.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges
split
chromosome
TxDb
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
jon.klonowski
▴ 40
4
votes
1
reply
742
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by
Hervé Pagès
16k • written 2.5 years ago by
Charles Plessy
▴ 180
0
votes
3
replies
5.2k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges
genomicra
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Alexandre
• 0
2
votes
4
replies
2.8k
views
How to simply change chromosome names of a GRanges object?
genomicrang
GenomicRanges
updated 2.3 years ago by
Hervé Pagès
16k • written 2.5 years ago by
changxu.fan
▴ 20
0
votes
2
replies
1.0k
views
Handling missing seqlenghts
GenomicRanges
2.5 years ago
Charles Plessy
▴ 180
4
votes
2
replies
1.2k
views
GenomicRanges::union fails on R devel
devel
GenomicRanges
2.6 years ago
Guillaume Devailly
▴ 60
5
votes
2
replies
1.1k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges
sesame
sesameData
GenomicFeatures
2.6 years ago
Pratik Mehta
▴ 10
2
votes
2
replies
1.2k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Junghoon
▴ 10
2
votes
2
replies
1.3k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.6 years ago
chirag.parsania
• 0
0
votes
2
replies
1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.7 years ago • updated 2.6 years ago
Arslan
• 0
0
votes
2
replies
946
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges
Genomic
2.7 years ago
Daniel Cameron
▴ 40
2
votes
4
replies
1.2k
views
Unique GPos taking into account mcols
GenomicRanges
unique
GPos
2.8 years ago • updated 2.6 years ago
maltethodberg
▴ 180
0
votes
1
reply
622
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
grr4006
• 0
0
votes
5
replies
2.6k
views
Grange object subsetting using seqnames
Seqnames
makeGRangesFromDataFrame
GRanges
Subsetting
GenomicRanges
2.8 years ago
rtrivedi1
▴ 10
0
votes
0
replies
668
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago
Dario Strbenac
★ 1.5k
3
votes
2
replies
783
views
Should I create a new class or using Common Classes
GenomicRanges
updated 2.9 years ago by
Hervé Pagès
16k • written 2.9 years ago by
Guandong Shang
▴ 40
0
votes
0
replies
714
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
3.0 years ago
alorsonmethyle
• 0
1
vote
4
replies
1.5k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges
GenomicRanges
3.0 years ago
Yixin
• 0
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.4 years ago • updated 3.3 years ago
rohitsatyam102
▴ 20
1
vote
1
reply
1.1k
views
cannot create GRanges object anymore
GenomicR
GenomicRanges
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
zhezhen
• 0
1
vote
1
reply
894
views
Average coverage between multiple samples
GenomicRanges
updated 3.4 years ago by
Michael Lawrence
★ 11k • written 3.4 years ago by
Jake
▴ 90
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.2 years ago by
jon.klonowski
▴ 40 • written 7.9 years ago by
endrebak85
▴ 40
1
vote
1
reply
1.2k
views
GenomicRanges equivalent to bedtools cluster
IRanges
GenomicRanges
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
kalamari
• 0
1
vote
3
replies
1.9k
views
Merging Neighboring Genomic Segments
Granges
GenomicRanges
3.5 years ago • updated 3.4 years ago
rahnaman
▴ 10
2
votes
2
replies
1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges
GenomeInfoDb
BSgenome
isCircular
updated 3.5 years ago by
Hervé Pagès
16k • written 3.6 years ago by
Chris Seidel
▴ 80
0
votes
0
replies
831
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr
GenomicRanges
3.5 years ago
Nala
• 0
0
votes
0
replies
1.2k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
3.6 years ago
r.a.policastro
• 0
50 results • Page
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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