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Showing :
rtracklayer
•
reset
0
votes
5
replies
866
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 8 months ago by
Aichatou
• 0
0
votes
4
replies
736
views
rtracklayer accessing UCSC data table not working
UCSC
rtracklayer
getTable
11 months ago
Andreas.Herbst
• 0
1
vote
2
replies
705
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
18 months ago
thomas
• 0
0
votes
4
replies
2.0k
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 18 months ago by
shepherl
4.2k • written 18 months ago by
Lucille
• 0
9
votes
38
replies
9.7k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 9.6 years ago by
tangming2005
▴ 200
2
votes
7
replies
1.2k
views
distanceToNearest
rtracklayer
ranges
distanceToNearest
20 months ago • updated 19 months ago
robjohn70000
• 0
1
vote
0
replies
937
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
22 months ago
yujin
▴ 10
1
vote
3
replies
1.1k
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer
Gviz
updated 22 months ago by
Hervé Pagès
16k • written 22 months ago by
yujin
▴ 10
1
vote
1
reply
1.2k
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 22 months ago by
Hervé Pagès
16k • written 22 months ago by
Anna
▴ 10
0
votes
18
replies
3.7k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 4.5 years ago by
lea
• 0
0
votes
0
replies
1.3k
views
Problem with loading rtracklayer
rtracklayer
updated 2.5 years ago by
shepherl
4.2k • written 2.5 years ago by
jiahe.janet
• 0
0
votes
0
replies
755
views
rtracklayer ignores ranges argument
rtracklayer
2.6 years ago
Kyle
• 0
0
votes
0
replies
999
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
2.6 years ago
Delta._.43
▴ 20
2
votes
3
replies
2.9k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal
ensembldb
rtracklayer
Annotation
updated 2.6 years ago by
rbj
• 0 • written 2.8 years ago by
Jake
▴ 10
3
votes
4
replies
2.0k
views
Convert a bed file to bigBed with rtracklayer
bed
bigBed
rtracklayer
ucsc
2.8 years ago
L
▴ 50
1
vote
3
replies
1.6k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 3.0 years ago by
ATpoint
★ 4.9k • written 3.0 years ago by
Mikhail Dozmorov
▴ 30
2
votes
2
replies
1.2k
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19
rtracklayer
AnnotationHub
3.0 years ago
Lenny186
• 0
0
votes
1
reply
953
views
rtracklayer import only subset of ranges
rtracklayer
updated 3.0 years ago by
shepherl
4.2k • written 3.0 years ago by
Jake
▴ 90
4
votes
5
replies
8.8k
views
Convert an R data.frame to a bed file in R
rtracklayer
R
bed
updated 2.6 years ago by
Walters
• 0 • written 3.1 years ago by
L
▴ 50
0
votes
8
replies
2.8k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.9 years ago by
Ruoyun
• 0 • written 3.1 years ago by
bonob
• 0
0
votes
1
reply
1.6k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Johanna
• 0
1
vote
2
replies
2.3k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
3.4 years ago
vanbelj
▴ 30
0
votes
1
reply
992
views
Rtracklayer
rtracklayer
RNASeq
gff
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
edusbioinfo
• 0
1
vote
4
replies
1.7k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer
GenomeInfoDb
3.7 years ago
Ge Tan
▴ 20
0
votes
2
replies
2.6k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw
rtracklayer
Windows
http
3.8 years ago
sla
• 0
0
votes
4
replies
2.1k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer
Visualization
updated 3.8 years ago by
Hervé Pagès
16k • written 3.8 years ago by
chase.mateusiak
• 0
0
votes
0
replies
952
views
Bug in rtracklayer
rtracklayer
3.8 years ago
You
• 0
2
votes
4
replies
1.6k
views
default behaviour of import.bw
import.bw
rtracklayer
3.8 years ago
Yixin
• 0
0
votes
2
replies
1.5k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
4.0 years ago
Arslan
• 0
0
votes
0
replies
887
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
4.0 years ago
Charles
• 0
2
votes
3
replies
2.5k
views
Importing a bed file
rtracklayer
4.3 years ago
Skylar
• 0
0
votes
1
reply
1.5k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
nick.shrine
• 0
2
votes
3
replies
2.4k
views
liftOver bug, reproducible
liftOver
rtracklayer
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
Mikhail Dozmorov
▴ 30
5
votes
5
replies
5.0k
views
Issues with installation status of R package rtracklayer
rtracklayer
Bioconductor
updated 3.6 years ago by
shepherl
4.2k • written 4.7 years ago by
svlachavas
▴ 840
1
vote
5
replies
6.2k
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 4.8 years ago by
Michael Lawrence
★ 11k • written 4.8 years ago by
Søren
• 0
2
votes
0
replies
1.5k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
4.8 years ago
Mikhail Dozmorov
▴ 30
9
votes
9
replies
6.4k
views
Importing a BED file with floating point scores?
rtracklayer
bed
updated 4.6 years ago by
merv
▴ 150 • written 9.4 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
0
replies
1.1k
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage
rtracklayer
4.8 years ago
David
• 0
2
votes
2
replies
1.8k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 5.3 years ago by
Hervé Pagès
16k • written 5.3 years ago by
Robert
▴ 10
1
vote
1
reply
3.1k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer
genomicranges
granges
updated 5.4 years ago by
Michael Lawrence
★ 11k • written 5.4 years ago by
ssabri
▴ 20
7
votes
16
replies
4.8k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores
granges
phastCons100way.UCSC.hg38
r
rtracklayer
updated 9 months ago by
rania.alanany
• 0 • written 5.5 years ago by
Biologist
▴ 120
2
votes
6
replies
3.2k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer
bigwig file
updated 3.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 5.5 years ago by
mzwanelen
▴ 10
0
votes
1
reply
1.1k
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 5.5 years ago by
Michael Lawrence
★ 11k • written 5.5 years ago by
prabin.dm
• 0
1
vote
1
reply
984
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 5.5 years ago by
Michael Lawrence
★ 11k • written 5.6 years ago by
alexis.weinreb
• 0
0
votes
0
replies
1.5k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools
rtracklayer
5.8 years ago
ATpoint
★ 4.9k
1
vote
2
replies
1.2k
views
rtracklayer::export empty score
rtracklayer
updated 5.8 years ago by
Michael Lawrence
★ 11k • written 5.8 years ago by
dinocolmillo
• 0
0
votes
4
replies
2.1k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges
rtracklayer
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
jovel_juan
▴ 30
0
votes
0
replies
990
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer
IRanges
DMDeepm6A
5.8 years ago
jovel_juan
▴ 30
2
votes
3
replies
2.1k
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 6.1 years ago by
Steve Lianoglou
★ 13k • written 6.1 years ago by
james.dalgleish
▴ 30
0
votes
1
reply
1.3k
views
rtracklayer import bigwig error
rtracklayer
updated 2.6 years ago by
Delta._.43
▴ 20 • written 6.2 years ago by
ribioinfo
▴ 100
262 results • Page
1 of 6
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel
by
James W. MacDonald
68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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