Showing : rtracklayer • reset
0
votes
4
replies
386
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
11 weeks ago • updated 10 weeks ago Andreas.Herbst • 0
1
vote
2
replies
517
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
9 months ago thomas • 0
0
votes
4
replies
1.3k
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 9 months ago by 4.1k • written 9 months ago by • 0
9
votes
38
replies
8.2k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.8 years ago by ▴ 200
2
votes
7
replies
920
views
distanceToNearest
rtracklayer ranges distanceToNearest
11 months ago robjohn70000 • 0
1
vote
0
replies
739
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
13 months ago yujin ▴ 10
1
vote
3
replies
848
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 13 months ago by 16k • written 13 months ago by ▴ 10
1
vote
1
reply
906
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 13 months ago by 16k • written 13 months ago by ▴ 10
0
votes
18
replies
3.1k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.8 years ago by • 0
0
votes
0
replies
1.1k
views
Problem with loading rtracklayer
rtracklayer
updated 22 months ago by 4.1k • written 22 months ago by • 0
0
votes
0
replies
634
views
rtracklayer ignores ranges argument
rtracklayer
22 months ago Kyle • 0
0
votes
0
replies
847
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
22 months ago Delta._.43 ▴ 20
2
votes
3
replies
2.3k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 22 months ago by • 0 • written 2.0 years ago by ▴ 10
3
votes
4
replies
1.6k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
2.1 years ago L ▴ 50
1
vote
3
replies
1.2k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by ▴ 30
2
votes
2
replies
994
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
2.3 years ago Lenny186 • 0
0
votes
1
reply
803
views
rtracklayer import only subset of ranges
rtracklayer
updated 2.3 years ago by 4.1k • written 2.3 years ago by ▴ 90
4
votes
5
replies
7.2k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 23 months ago by • 0 • written 2.4 years ago by ▴ 50
0
votes
8
replies
2.3k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.1 years ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
1.3k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
1
vote
2
replies
1.9k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.6 years ago vanbelj ▴ 30
0
votes
1
reply
850
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
1
vote
4
replies
1.4k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
3.0 years ago Ge Tan ▴ 20
0
votes
2
replies
2.3k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw rtracklayer Windows http
3.0 years ago sla • 0
0
votes
4
replies
1.8k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
0
votes
0
replies
759
views
Bug in rtracklayer
rtracklayer
3.1 years ago You • 0
2
votes
4
replies
1.4k
views
default behaviour of import.bw
import.bw rtracklayer
3.1 years ago Yixin • 0
0
votes
2
replies
1.3k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
3.3 years ago Arslan • 0
0
votes
0
replies
764
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
3.3 years ago Charles • 0
2
votes
3
replies
2.1k
views
Importing a bed file
rtracklayer
3.5 years ago Skylar • 0
0
votes
1
reply
1.3k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
2
votes
3
replies
1.9k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 3.8 years ago by 67k • written 3.8 years ago by ▴ 30
5
votes
5
replies
4.1k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.8 years ago by 4.1k • written 3.9 years ago by ▴ 840
1
vote
5
replies
5.1k
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 4.0 years ago by ★ 11k • written 4.0 years ago by • 0
2
votes
0
replies
1.2k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
4.0 years ago Mikhail Dozmorov ▴ 30
9
votes
9
replies
5.9k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.8 years ago by ▴ 140 • written 8.7 years ago by ★ 7.9k
0
votes
0
replies
964
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.1 years ago David • 0
2
votes
2
replies
1.5k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.6 years ago by 16k • written 4.6 years ago by ▴ 10
1
vote
1
reply
2.7k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.7 years ago by ★ 11k • written 4.7 years ago by ▴ 20
7
votes
16
replies
4.0k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 23 days ago by • 0 • written 4.7 years ago by ▴ 120
2
votes
6
replies
2.6k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.2 years ago by ★ 1.1k • written 4.8 years ago by ▴ 10
0
votes
1
reply
967
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 4.8 years ago by ★ 11k • written 4.8 years ago by • 0
1
vote
1
reply
797
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 4.8 years ago by ★ 11k • written 4.8 years ago by • 0
0
votes
0
replies
1.3k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
5.1 years ago • updated 5.0 years ago ATpoint ★ 4.6k
1
vote
2
replies
1.0k
views
rtracklayer::export empty score
rtracklayer
updated 5.1 years ago by ★ 11k • written 5.1 years ago by • 0
0
votes
4
replies
1.9k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 5.1 years ago by 67k • written 5.1 years ago by ▴ 30
0
votes
0
replies
878
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.1 years ago jovel_juan ▴ 30
2
votes
3
replies
1.7k
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 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 30
0
votes
1
reply
1.2k
views
rtracklayer import bigwig error
rtracklayer
updated 22 months ago by ▴ 20 • written 5.4 years ago by ▴ 100
0
votes
1
reply
1.3k
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe by ATpoint ★ 4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe by swbarnes2 ★ 1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
Comment: RSubread output significantly different from bash Subread output by Aimee • 0
Hi Gordon, Thank you so much for this response. I went back and checked, and you are absolutely correct that it was shown in the settings b…
Answer: Can we get beta values with DMRcate package by James W. MacDonald 67k
If you get an error that says ``` Error in getCollapsedBetas(myAnnotation) : could not find function "getCollapsedBetas" ``` It …
Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k
I think this already happened, see https://github.com/nf-core/rnasplice/issues/162
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: Running multiple KNN queries in parallel
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Teacher to Gordon Smyth 52k
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