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Showing :
genomicranges
•
reset
4
votes
2
replies
974
views
GAlignments Cigar to GRanges
GenomicRanges
cigarRangesAlongReferenceSpace
GenomicAlignments
Cigar
5 days ago • updated 4 days ago
pineiroalejandro
▴ 10
0
votes
0
replies
248
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
22 days ago
jamiecatalano2
• 0
0
votes
2
replies
779
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
26 days ago • updated 4 days ago
Kateřina
• 0
1
vote
4
replies
853
views
fast apply on RleList
GenomicRanges
RleList
5 weeks ago
story.benjamin
▴ 20
2
votes
1
reply
883
views
Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges
CNEr
5 weeks ago
1324087964
• 0
0
votes
1
reply
1.1k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
updated 3 months ago by
Michael Love
43k • written 4.0 years ago by
alorsonmethyle
• 0
1
vote
1
reply
1.7k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
updated 3 months ago by
Michael Love
43k • written 4.6 years ago by
r.a.policastro
• 0
0
votes
0
replies
247
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
6 months ago
info
▴ 10
3
votes
3
replies
590
views
ISO a solution to rank-order introns by transcript
GenomicRanges
GenomicFeatures
7 months ago • updated 5 months ago
mat149
▴ 80
0
votes
0
replies
374
views
hichip fragments extraction chip seq
ChIPSeqData
interact
GenomicRanges
HiC
9 months ago
user_bioinfo
• 0
2
votes
1
reply
480
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 12 months ago by
Michael Love
43k • written 12 months ago by
mat149
▴ 80
0
votes
0
replies
525
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
14 months ago
gshweta95
• 0
0
votes
0
replies
527
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
15 months ago
mat149
▴ 80
2
votes
1
reply
720
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
15 months ago
mat149
▴ 80
0
votes
2
replies
1.2k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2
Bioconductor
GenomicRanges
updated 2.0 years ago by
Virginie
• 0 • written 2.1 years ago by
gs12
• 0
3
votes
4
replies
1.6k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges
IRanges
updated 2.2 years ago by
Hervé Pagès
16k • written 2.2 years ago by
jbendik
• 0
0
votes
1
reply
1.0k
views
Error printing a CompressedGRangesList
GenomicRanges
2.4 years ago • updated 2.2 years ago
Lluís Revilla Sancho
▴ 760
0
votes
0
replies
940
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
2.3 years ago
Delta._.43
▴ 20
4
votes
4
replies
2.2k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Dario Strbenac
★ 1.6k
3
votes
1
reply
1.0k
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges
GenomicRanges
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
d.s.h.andel-3
• 0
0
votes
2
replies
1.9k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 2.5 years ago by
Malcolm Cook
★ 1.6k • written 2.5 years ago by
mike-zx
• 0
2
votes
2
replies
3.0k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
2.6 years ago
Mog
• 0
0
votes
0
replies
803
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.9 years ago
Simon Coetzee
▴ 50
2
votes
3
replies
2.9k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges
plyranges
2.9 years ago
Rodrigo
• 0
0
votes
1
reply
1.5k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
Johanna
• 0
3
votes
2
replies
2.0k
views
toGRanges help!
GenomicRanges
toGRanges
Bioconductor
3.0 years ago
samantha.haque
• 0
1
vote
2
replies
2.2k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
3.1 years ago
vanbelj
▴ 30
0
votes
1
reply
1.5k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 3.1 years ago by
Basti
▴ 780 • written 3.1 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
1.1k
views
How about a getSeq() method for GRanges ?
GenomicRanges
BSGenome
3.1 years ago
Charles Plessy
▴ 180
0
votes
2
replies
5.5k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 3.1 years ago by
kent.riemondy
▴ 20 • written 3.2 years ago by
svenbioinf
• 0
0
votes
6
replies
2.2k
views
Error: duplicate row.names
GenomicRanges
methylKit
S4Vectors
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
hasche
• 0
0
votes
0
replies
1.1k
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation
CNVRanger
GenomicRanges
3.3 years ago
svlachavas
▴ 840
6
votes
2
replies
1.7k
views
strand-aware GRanges shift
GenomicRanges
updated 3.3 years ago by
Malcolm Cook
★ 1.6k • written 3.3 years ago by
gene_bioconductor
▴ 10
9
votes
9
replies
4.8k
views
Subset GRanges by intersection
findOverlaps
GPos
GenomicRanges
subsetByOverlaps
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Robert
▴ 10
3
votes
5
replies
2.6k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges
split
chromosome
TxDb
updated 3.4 years ago by
Hervé Pagès
16k • written 3.4 years ago by
jon.klonowski
▴ 40
4
votes
1
reply
1.0k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.5 years ago by
Hervé Pagès
16k • written 3.5 years ago by
Charles Plessy
▴ 180
1
vote
3
replies
7.7k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges
genomicra
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Alexandre
▴ 10
2
votes
4
replies
4.4k
views
How to simply change chromosome names of a GRanges object?
genomicrang
GenomicRanges
updated 3.4 years ago by
Hervé Pagès
16k • written 3.6 years ago by
changxu.fan
▴ 20
0
votes
2
replies
1.6k
views
Handling missing seqlenghts
GenomicRanges
3.6 years ago
Charles Plessy
▴ 180
4
votes
2
replies
1.5k
views
GenomicRanges::union fails on R devel
devel
GenomicRanges
3.6 years ago
Guillaume Devailly
▴ 60
5
votes
2
replies
1.5k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges
sesame
sesameData
GenomicFeatures
3.7 years ago
Pratik Mehta
▴ 10
2
votes
2
replies
1.7k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
Junghoon
▴ 10
3
votes
2
replies
1.9k
views
`GenomicRanges` cheat sheet
GenomicRanges
3.7 years ago
chirag.parsania
▴ 10
0
votes
2
replies
1.4k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
3.7 years ago
Arslan
• 0
0
votes
2
replies
1.3k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges
Genomic
3.8 years ago
Daniel Cameron
▴ 40
2
votes
4
replies
1.6k
views
Unique GPos taking into account mcols
GenomicRanges
unique
GPos
3.8 years ago • updated 3.7 years ago
maltethodberg
▴ 180
0
votes
1
reply
908
views
How to overlap granges objects by gene name
GenomicRanges
updated 3.8 years ago by
James W. MacDonald
68k • written 3.8 years ago by
grr4006
• 0
0
votes
5
replies
4.2k
views
Grange object subsetting using seqnames
Seqnames
makeGRangesFromDataFrame
GRanges
Subsetting
GenomicRanges
3.9 years ago
rtrivedi1
▴ 10
0
votes
0
replies
890
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.9 years ago
Dario Strbenac
★ 1.6k
3
votes
2
replies
1.2k
views
Should I create a new class or using Common Classes
GenomicRanges
updated 4.0 years ago by
Hervé Pagès
16k • written 4.0 years ago by
Guandong Shang
▴ 40
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Comment: Limma trend with limpa
by
Alejandro
• 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error
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asafpr
• 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Comment: Discrepancies in normalised count data vs unnormalised
by
AMgroup
• 0
Thank you for your reply! There are some pretty big discrepancies in the total raw counts between samples: ![enter image description here…
Answer: Limma trend with limpa
by
Gordon Smyth
52k
Dear Alejandro, Thanks for your interest. No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …
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52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
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Answer: Check removeBatchEffect effectiveness
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GAlignments Cigar to GRanges
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