Showing : rtracklayer • reset
1
vote
2
replies
291
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
12 weeks ago thomas • 0
0
votes
4
replies
468
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 3 months ago by 3.9k • written 3 months ago by • 0
2
votes
7
replies
555
views
distanceToNearest
rtracklayer ranges distanceToNearest
4 months ago robjohn70000 • 0
1
vote
0
replies
478
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
7 months ago yujin ▴ 10
1
vote
3
replies
636
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 7 months ago by 16k • written 7 months ago by ▴ 10
1
vote
1
reply
520
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 7 months ago by 16k • written 7 months ago by ▴ 10
0
votes
0
replies
776
views
Problem with loading rtracklayer
rtracklayer
updated 15 months ago by 3.9k • written 15 months ago by • 0
0
votes
0
replies
516
views
rtracklayer ignores ranges argument
rtracklayer
16 months ago Kyle • 0
0
votes
0
replies
626
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
16 months ago Delta._.43 ▴ 20
2
votes
3
replies
1.8k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 16 months ago by • 0 • written 18 months ago by ▴ 10
3
votes
4
replies
1.2k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
18 months ago L ▴ 50
1
vote
3
replies
926
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 20 months ago by ★ 4.2k • written 20 months ago by ▴ 30
2
votes
2
replies
796
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
21 months ago Lenny186 • 0
0
votes
1
reply
607
views
rtracklayer import only subset of ranges
rtracklayer
updated 21 months ago by 3.9k • written 21 months ago by ▴ 90
4
votes
5
replies
5.7k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 16 months ago by • 0 • written 22 months ago by ▴ 50
0
votes
8
replies
1.9k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 19 months ago by • 0 • written 22 months ago by • 0
0
votes
1
reply
1.0k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 23 months ago by 66k • written 23 months ago by • 0
1
vote
2
replies
1.6k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.1 years ago vanbelj ▴ 30
0
votes
1
reply
709
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.2 years ago by 66k • written 2.2 years ago by • 0
1
vote
4
replies
1.1k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
2.5 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
2.5 years ago sla • 0
0
votes
0
replies
569
views
Bug in rtracklayer
rtracklayer
2.6 years ago You • 0
0
votes
4
replies
1.4k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
2
votes
4
replies
1.2k
views
default behaviour of import.bw
import.bw rtracklayer
2.6 years ago Yixin • 0
0
votes
2
replies
1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.7 years ago Arslan • 0
0
votes
0
replies
633
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
2.7 years ago Charles • 0
2
votes
3
replies
1.8k
views
Importing a bed file
rtracklayer
3.0 years ago Skylar • 0
0
votes
1
reply
1.2k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.1 years ago by 66k • written 3.1 years ago by • 0
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
2
votes
3
replies
1.7k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 3.3 years ago by 66k • written 3.3 years ago by ▴ 30
5
votes
5
replies
3.3k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.3 years ago by 3.9k • written 3.4 years ago by ▴ 830
1
vote
5
replies
4.1k
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 3.5 years ago by ★ 11k • written 3.5 years ago by • 0
2
votes
0
replies
996
views
How to liftOver Paired BED (bedpe) data
rtracklayer
3.5 years ago Mikhail Dozmorov ▴ 30
0
votes
0
replies
745
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
3.6 years ago David • 0
2
votes
2
replies
1.3k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 10
1
vote
1
reply
2.3k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.1 years ago by ★ 11k • written 4.1 years ago by ▴ 20
7
votes
13
replies
2.6k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4.2 years ago by ★ 3.3k • written 4.2 years ago by ▴ 110
2
votes
6
replies
2.0k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 2.7 years ago by ★ 1.1k • written 4.2 years ago by ▴ 10
0
votes
1
reply
820
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 4.2 years ago by ★ 11k • written 4.2 years ago by • 0
1
vote
1
reply
655
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 4.3 years ago by ★ 11k • written 4.3 years ago by • 0
0
votes
0
replies
1.1k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
4.5 years ago ATpoint ★ 4.2k
1
vote
2
replies
862
views
rtracklayer::export empty score
rtracklayer
updated 4.5 years ago by ★ 11k • written 4.5 years ago by • 0
0
votes
4
replies
1.7k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 4.6 years ago by 66k • written 4.6 years ago by ▴ 30
0
votes
0
replies
751
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
4.6 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 4.9 years ago by ★ 13k • written 4.9 years ago by ▴ 30
0
votes
1
reply
958
views
rtracklayer import bigwig error
rtracklayer
updated 16 months ago by ▴ 20 • written 4.9 years ago by ▴ 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 5.1 years ago by 16k • written 5.1 years ago by ▴ 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 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 180
2
votes
7
replies
1.2k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 5.2 years ago by ★ 11k • written 5.3 years ago by ▴ 100
0
votes
4
replies
1.1k
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 5.3 years ago by 66k • written 5.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
Votes
Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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