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Showing :
rtracklayer
•
reset
1
vote
2
replies
231
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
6 weeks ago
thomas
• 0
0
votes
4
replies
290
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 8 weeks ago by
shepherl
3.8k • written 8 weeks ago by
Lucille
• 0
9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 8.2 years ago by
tangming2005
▴ 190
0
votes
21
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
2
votes
7
replies
470
views
distanceToNearest
rtracklayer
ranges
distanceToNearest
3 months ago
robjohn70000
• 0
1
vote
3
replies
579
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer
Gviz
updated 5 months ago by
Hervé Pagès
16k • written 5 months ago by
yujin
▴ 10
1
vote
0
replies
419
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
5 months ago
yujin
▴ 10
1
vote
1
reply
442
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 5 months ago by
Hervé Pagès
16k • written 6 months ago by
Anna
▴ 10
0
votes
0
replies
689
views
Problem with loading rtracklayer
rtracklayer
updated 14 months ago by
shepherl
3.8k • written 14 months ago by
jiahe.janet
• 0
0
votes
0
replies
487
views
rtracklayer ignores ranges argument
rtracklayer
14 months ago
Kyle
• 0
2
votes
3
replies
1.7k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal
ensembldb
rtracklayer
Annotation
updated 15 months ago by
rbj
• 0 • written 17 months ago by
Jake
▴ 10
0
votes
0
replies
566
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
15 months ago
Delta._.43
▴ 20
0
votes
1
reply
898
views
rtracklayer import bigwig error
rtracklayer
updated 15 months ago by
Delta._.43
▴ 20 • written 4.8 years ago by
ribioinfo
▴ 100
4
votes
5
replies
5.4k
views
Convert an R data.frame to a bed file in R
rtracklayer
R
bed
updated 15 months ago by
Walters
• 0 • written 21 months ago by
L
▴ 50
3
votes
4
replies
1.1k
views
Convert a bed file to bigBed with rtracklayer
bed
bigBed
rtracklayer
ucsc
17 months ago
L
▴ 50
0
votes
8
replies
1.8k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 18 months ago by
Ruoyun
• 0 • written 21 months ago by
bonob
• 0
1
vote
3
replies
848
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
Mikhail Dozmorov
▴ 30
2
votes
2
replies
749
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19
rtracklayer
AnnotationHub
20 months ago • updated 19 months ago
Lenny186
• 0
0
votes
1
reply
572
views
rtracklayer import only subset of ranges
rtracklayer
updated 20 months ago by
shepherl
3.8k • written 20 months ago by
Jake
▴ 90
0
votes
1
reply
935
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
2
votes
4
replies
5.9k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist
rtracklayer
updated 22 months ago by
James
• 0 • written 8.8 years ago by
Jake
▴ 90
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
24 months ago
vanbelj
▴ 30
0
votes
1
reply
684
views
Rtracklayer
rtracklayer
RNASeq
gff
updated 2.0 years ago by
James W. MacDonald
65k • written 2.0 years ago by
edusbioinfo
• 0
5
votes
5
replies
3.2k
views
Issues with installation status of R package rtracklayer
rtracklayer
Bioconductor
updated 2.2 years ago by
shepherl
3.8k • written 3.3 years ago by
svlachavas
▴ 830
1
vote
4
replies
1.1k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer
GenomeInfoDb
2.4 years ago
Ge Tan
▴ 20
0
votes
2
replies
1.9k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw
rtracklayer
Windows
http
2.4 years ago
sla
• 0
0
votes
4
replies
1.4k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer
Visualization
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
chase.mateusiak
• 0
2
votes
4
replies
1.1k
views
default behaviour of import.bw
import.bw
rtracklayer
2.5 years ago • updated 2.4 years ago
Yixin
• 0
0
votes
0
replies
540
views
Bug in rtracklayer
rtracklayer
2.4 years ago
You
• 0
2
votes
6
replies
1.9k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer
bigwig file
updated 2.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.1 years ago by
mzwanelen
▴ 10
0
votes
2
replies
1.0k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.6 years ago
Arslan
• 0
0
votes
0
replies
605
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
2.6 years ago
Charles
• 0
2
votes
3
replies
1.7k
views
Importing a bed file
rtracklayer
2.9 years ago
Skylar
• 0
0
votes
1
reply
1.1k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
nick.shrine
• 0
2
votes
3
replies
1.6k
views
liftOver bug, reproducible
liftOver
rtracklayer
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
Mikhail Dozmorov
▴ 30
9
votes
9
replies
5.3k
views
Importing a BED file with floating point scores?
rtracklayer
bed
updated 3.2 years ago by
merv
▴ 120 • written 8.0 years ago by
Ryan C. Thompson
★ 7.9k
1
vote
4
replies
2.4k
views
Import Chain - Cannot Import Chain File
rtracklayer
updated 3.3 years ago by
athief
▴ 20 • written 5.7 years ago by
kipperf
• 0
1
vote
5
replies
3.9k
views
RStudio vs R: using rtracklayer to import bigwig files from http works in R but not in RStudio.
import.bw
rtracklayer
http
RStudio
updated 3.4 years ago by
Michael Lawrence
★ 11k • written 3.4 years ago by
Søren
• 0
2
votes
0
replies
951
views
How to liftOver Paired BED (bedpe) data
rtracklayer
3.4 years ago
Mikhail Dozmorov
▴ 30
0
votes
0
replies
710
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage
rtracklayer
3.4 years ago
David
• 0
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 3.9 years ago by
Hervé Pagès
16k • written 3.9 years ago by
Robert
▴ 10
1
vote
1
reply
2.2k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer
genomicranges
granges
updated 4.0 years ago by
Michael Lawrence
★ 11k • written 4.0 years ago by
ssabri
▴ 20
7
votes
13
replies
2.5k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores
granges
phastCons100way.UCSC.hg38
r
rtracklayer
updated 4.1 years ago by
Robert Castelo
★ 3.2k • written 4.1 years ago by
Biologist
▴ 110
0
votes
1
reply
758
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 4.1 years ago by
Michael Lawrence
★ 11k • written 4.1 years ago by
prabin.dm
• 0
1
vote
1
reply
624
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 4.2 years ago by
Michael Lawrence
★ 11k • written 4.2 years ago by
alexis.weinreb
• 0
0
votes
0
replies
1.1k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools
rtracklayer
4.4 years ago
ATpoint
★ 4.0k
1
vote
2
replies
829
views
rtracklayer::export empty score
rtracklayer
updated 4.4 years ago by
Michael Lawrence
★ 11k • written 4.4 years ago by
dinocolmillo
• 0
0
votes
4
replies
1.6k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges
rtracklayer
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
jovel_juan
▴ 30
0
votes
0
replies
722
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer
IRanges
DMDeepm6A
4.5 years ago
jovel_juan
▴ 30
2
votes
3
replies
1.5k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges
rtracklayer
VariantAnnotation
S4Vectors
SummarizedExperiment
updated 4.8 years ago by
Steve Lianoglou
★ 13k • written 4.8 years ago by
james.dalgleish
▴ 30
50 results • Page
1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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