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Showing :
GenomicRanges
•
reset
0
votes
0
replies
141
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
4 weeks ago
mat149
▴ 70
2
votes
1
reply
198
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
6 weeks ago
mat149
▴ 70
0
votes
2
replies
703
views
GenomicRanges coult not be loaded after R upgrade
DESeq2
Bioconductor
GenomicRanges
updated 10 months ago by
Virginie
• 0 • written 10 months ago by
gs12
• 0
3
votes
4
replies
828
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges
IRanges
updated 12 months ago by
Hervé Pagès
16k • written 12 months ago by
jbendik
• 0
0
votes
1
reply
567
views
Error printing a CompressedGRangesList
GenomicRanges
14 months ago • updated 12 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
509
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
14 months ago
Delta._.43
▴ 20
4
votes
4
replies
1.1k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Dario Strbenac
★ 1.5k
3
votes
1
reply
660
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges
GenomicRanges
updated 15 months ago by
Michael Love
41k • written 15 months ago by
d.s.h.andel-3
• 0
0
votes
2
replies
1.0k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 16 months ago by
Malcolm Cook
★ 1.6k • written 16 months ago by
mike-zx
• 0
2
votes
2
replies
1.6k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
17 months ago
Mog
• 0
0
votes
0
replies
543
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
20 months ago
Simon Coetzee
▴ 50
2
votes
3
replies
1.6k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges
plyranges
20 months ago
Rodrigo
• 0
0
votes
1
reply
878
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
Johanna
• 0
3
votes
2
replies
1.2k
views
toGRanges help!
GenomicRanges
toGRanges
Bioconductor
22 months ago
samantha.haque
• 0
1
vote
2
replies
1.4k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
23 months ago
vanbelj
▴ 20
0
votes
1
reply
895
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 23 months ago by
Basti
▴ 750 • written 23 months ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
725
views
How about a getSeq() method for GRanges ?
GenomicRanges
BSGenome
23 months ago
Charles Plessy
▴ 180
0
votes
2
replies
3.4k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 23 months ago by
kent.riemondy
▴ 20 • written 2.0 years ago by
svenbioinf
• 0
0
votes
6
replies
1.4k
views
Error: duplicate row.names
GenomicRanges
methylKit
S4Vectors
updated 24 months ago by
James W. MacDonald
65k • written 24 months ago by
hasche
• 0
0
votes
0
replies
625
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation
CNVRanger
GenomicRanges
2.1 years ago
svlachavas
▴ 830
6
votes
2
replies
1.1k
views
strand-aware GRanges shift
GenomicRanges
updated 2.1 years ago by
Malcolm Cook
★ 1.6k • written 2.1 years ago by
gene_bioconductor
▴ 10
9
votes
9
replies
3.0k
views
Subset GRanges by intersection
findOverlaps
GPos
GenomicRanges
subsetByOverlaps
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Robert
▴ 10
3
votes
5
replies
1.7k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges
split
chromosome
TxDb
updated 2.3 years ago by
Hervé Pagès
16k • written 2.3 years ago by
jon.klonowski
▴ 40
4
votes
1
reply
695
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.3 years ago by
Hervé Pagès
16k • written 2.3 years ago by
Charles Plessy
▴ 180
0
votes
3
replies
4.9k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges
genomicra
updated 2.4 years ago by
James W. MacDonald
65k • written 2.4 years ago by
Alexandre
• 0
2
votes
4
replies
2.6k
views
How to simply change chromosome names of a GRanges object?
genomicrang
GenomicRanges
updated 2.2 years ago by
Hervé Pagès
16k • written 2.4 years ago by
changxu.fan
▴ 20
0
votes
2
replies
973
views
Handling missing seqlenghts
GenomicRanges
2.4 years ago
Charles Plessy
▴ 180
4
votes
2
replies
1.2k
views
GenomicRanges::union fails on R devel
devel
GenomicRanges
2.5 years ago
Guillaume Devailly
▴ 60
5
votes
2
replies
1.0k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges
sesame
sesameData
GenomicFeatures
2.5 years ago
Pratik Mehta
▴ 10
2
votes
2
replies
1.1k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Junghoon
▴ 10
2
votes
2
replies
1.3k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.5 years ago
chirag.parsania
• 0
0
votes
2
replies
995
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.5 years ago
Arslan
• 0
0
votes
2
replies
884
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges
Genomic
2.6 years ago
Daniel Cameron
▴ 40
2
votes
4
replies
1.1k
views
Unique GPos taking into account mcols
GenomicRanges
unique
GPos
2.6 years ago • updated 2.5 years ago
maltethodberg
▴ 170
0
votes
1
reply
593
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
grr4006
• 0
0
votes
5
replies
2.4k
views
Grange object subsetting using seqnames
Seqnames
makeGRangesFromDataFrame
GRanges
Subsetting
GenomicRanges
2.7 years ago
rtrivedi1
▴ 10
0
votes
0
replies
641
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.8 years ago
Dario Strbenac
★ 1.5k
3
votes
2
replies
729
views
Should I create a new class or using Common Classes
GenomicRanges
updated 2.8 years ago by
Hervé Pagès
16k • written 2.8 years ago by
Guandong Shang
▴ 40
0
votes
0
replies
672
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
2.9 years ago
alorsonmethyle
• 0
1
vote
4
replies
1.4k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges
GenomicRanges
2.9 years ago
Yixin
• 0
11
votes
13
replies
3.8k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.3 years ago • updated 3.1 years ago
rohitsatyam102
▴ 20
1
vote
1
reply
1.0k
views
cannot create GRanges object anymore
GenomicR
GenomicRanges
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
zhezhen
• 0
1
vote
1
reply
844
views
Average coverage between multiple samples
GenomicRanges
updated 3.2 years ago by
Michael Lawrence
★ 11k • written 3.3 years ago by
Jake
▴ 90
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.1 years ago by
jon.klonowski
▴ 40 • written 7.7 years ago by
endrebak85
▴ 30
1
vote
1
reply
1.2k
views
GenomicRanges equivalent to bedtools cluster
IRanges
GenomicRanges
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
kalamari
• 0
1
vote
3
replies
1.7k
views
Merging Neighboring Genomic Segments
Granges
GenomicRanges
3.3 years ago
rahnaman
▴ 10
2
votes
2
replies
1.4k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges
GenomeInfoDb
BSgenome
isCircular
updated 3.4 years ago by
Hervé Pagès
16k • written 3.5 years ago by
Chris Seidel
▴ 80
0
votes
0
replies
785
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr
GenomicRanges
3.4 years ago
Nala
• 0
0
votes
0
replies
1.1k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
3.4 years ago
r.a.policastro
• 0
0
votes
1
reply
1.0k
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements
IRanges
GenomicRanges
BSgenome
updated 3.6 years ago by
James W. MacDonald
65k • written 3.6 years ago by
vinod.acear
▴ 50
50 results • Page
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Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
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Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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