Showing : rtracklayer • reset
0
votes
5
replies
623
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 6 weeks ago by • 0
0
votes
4
replies
453
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
4 months ago Andreas.Herbst • 0
1
vote
2
replies
570
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
10 months ago thomas • 0
0
votes
4
replies
1.4k
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 11 months ago by 4.1k • written 11 months ago by • 0
9
votes
38
replies
8.5k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 9.0 years ago by ▴ 200
2
votes
7
replies
995
views
distanceToNearest
rtracklayer ranges distanceToNearest
12 months ago robjohn70000 • 0
1
vote
0
replies
779
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
15 months ago yujin ▴ 10
1
vote
3
replies
887
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 15 months ago by 16k • written 15 months ago by ▴ 10
1
vote
1
reply
960
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 15 months ago by 16k • written 15 months ago by ▴ 10
0
votes
18
replies
3.2k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.9 years ago by • 0
0
votes
0
replies
1.1k
views
Problem with loading rtracklayer
rtracklayer
updated 23 months ago by 4.1k • written 23 months ago by • 0
0
votes
0
replies
664
views
rtracklayer ignores ranges argument
rtracklayer
24 months ago Kyle • 0
0
votes
0
replies
874
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.0 years ago Delta._.43 ▴ 20
2
votes
3
replies
2.4k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 2.0 years ago by • 0 • written 2.2 years ago by ▴ 10
3
votes
4
replies
1.7k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
2.2 years ago L ▴ 50
1
vote
3
replies
1.3k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by ▴ 30
2
votes
2
replies
1.0k
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
2.4 years ago Lenny186 • 0
0
votes
1
reply
829
views
rtracklayer import only subset of ranges
rtracklayer
updated 2.4 years ago by 4.1k • written 2.4 years ago by ▴ 90
4
votes
5
replies
7.5k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.1 years ago by • 0 • written 2.5 years ago by ▴ 50
0
votes
8
replies
2.4k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.3 years ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
1.3k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
1
vote
2
replies
2.0k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.8 years ago vanbelj ▴ 30
0
votes
1
reply
878
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
1
vote
4
replies
1.4k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
3.1 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
3.2 years ago sla • 0
0
votes
4
replies
1.8k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
0
votes
0
replies
784
views
Bug in rtracklayer
rtracklayer
3.2 years ago You • 0
2
votes
4
replies
1.4k
views
default behaviour of import.bw
import.bw rtracklayer
3.2 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
3.4 years ago Arslan • 0
0
votes
0
replies
792
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
3.4 years ago Charles • 0
2
votes
3
replies
2.1k
views
Importing a bed file
rtracklayer
3.7 years ago Skylar • 0
0
votes
1
reply
1.4k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
2
votes
3
replies
2.0k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 30
5
votes
5
replies
4.3k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.0 years ago by 4.1k • written 4.1 years ago by ▴ 840
1
vote
5
replies
5.4k
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 4.2 years ago by ★ 11k • written 4.2 years ago by • 0
2
votes
0
replies
1.3k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
4.2 years ago Mikhail Dozmorov ▴ 30
9
votes
9
replies
6.0k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.0 years ago by ▴ 140 • written 8.8 years ago by ★ 7.9k
0
votes
0
replies
1.0k
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.2 years ago David • 0
2
votes
2
replies
1.6k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 10
1
vote
1
reply
2.8k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.8 years ago by ★ 11k • written 4.8 years ago by ▴ 20
7
votes
16
replies
4.1k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 10 weeks ago by • 0 • written 4.9 years ago by ▴ 120
2
votes
6
replies
2.7k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.3 years ago by ★ 1.1k • written 4.9 years ago by ▴ 10
0
votes
1
reply
996
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 4.9 years ago by ★ 11k • written 4.9 years ago by • 0
1
vote
1
reply
834
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 5.0 years ago by ★ 11k • written 5.0 years ago by • 0
0
votes
0
replies
1.4k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
5.2 years ago ATpoint ★ 4.6k
1
vote
2
replies
1.1k
views
rtracklayer::export empty score
rtracklayer
updated 5.2 years ago by ★ 11k • written 5.2 years ago by • 0
0
votes
4
replies
2.0k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 30
0
votes
0
replies
900
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.2 years ago jovel_juan ▴ 30
2
votes
3
replies
1.8k
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 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 30
0
votes
1
reply
1.2k
views
rtracklayer import bigwig error
rtracklayer
updated 2.0 years ago by ▴ 20 • written 5.6 years ago by ▴ 100
50 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
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