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Showing :
rtracklayer
•
reset
1
vote
2
replies
232
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
6 weeks ago
thomas
• 0
0
votes
4
replies
291
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
2
votes
7
replies
470
views
distanceToNearest
rtracklayer
ranges
distanceToNearest
3 months ago
robjohn70000
• 0
1
vote
0
replies
419
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
5 months ago
yujin
▴ 10
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
1
reply
442
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 6 months ago by
Hervé Pagès
16k • written 6 months ago by
Anna
▴ 10
0
votes
21
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
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
0
votes
0
replies
567
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
15 months ago
Delta._.43
▴ 20
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
3
votes
4
replies
1.1k
views
Convert a bed file to bigBed with rtracklayer
bed
bigBed
rtracklayer
ucsc
17 months ago
L
▴ 50
1
vote
3
replies
849
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
573
views
rtracklayer import only subset of ranges
rtracklayer
updated 20 months ago by
shepherl
3.8k • written 20 months ago by
Jake
▴ 90
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
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
0
votes
1
reply
936
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
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
685
views
Rtracklayer
rtracklayer
RNASeq
gff
updated 2.0 years ago by
James W. MacDonald
65k • written 2.0 years ago by
edusbioinfo
• 0
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
0
votes
0
replies
540
views
Bug in rtracklayer
rtracklayer
2.4 years ago
You
• 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
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
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
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
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
0
votes
0
replies
711
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
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
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
625
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
831
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
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
0
votes
1
reply
1.1k
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures
rtracklayer
updated 5.0 years ago by
Hervé Pagès
16k • written 5.0 years ago by
stephane.plaisance
▴ 10
4
votes
1
reply
1.1k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges
seqinfo
import.bw
BigWigFile
rtracklayer
updated 5.1 years ago by
Michael Lawrence
★ 11k • written 5.1 years ago by
maltethodberg
▴ 170
50 results • Page
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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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