Showing : rtracklayer • reset
0
votes
5
replies
649
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 10 weeks ago by • 0
0
votes
4
replies
496
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
5 months ago Andreas.Herbst • 0
1
vote
2
replies
582
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
11 months ago thomas • 0
0
votes
4
replies
1.5k
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 12 months ago by 4.1k • written 12 months ago by • 0
9
votes
38
replies
8.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 9.0 years ago by ▴ 200
2
votes
7
replies
1.0k
views
distanceToNearest
rtracklayer ranges distanceToNearest
13 months ago robjohn70000 • 0
1
vote
0
replies
808
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
15 months ago yujin ▴ 10
1
vote
3
replies
909
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 15 months ago by 16k • written 16 months ago by ▴ 10
1
vote
1
reply
990
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 16 months ago by 16k • written 16 months ago by ▴ 10
0
votes
18
replies
3.2k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 4.0 years ago by • 0
0
votes
0
replies
1.1k
views
Problem with loading rtracklayer
rtracklayer
updated 2.0 years ago by 4.1k • written 2.0 years ago by • 0
0
votes
0
replies
674
views
rtracklayer ignores ranges argument
rtracklayer
2.1 years ago Kyle • 0
0
votes
0
replies
891
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.1 years ago Delta._.43 ▴ 20
2
votes
3
replies
2.5k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 2.1 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
2.3 years ago L ▴ 50
1
vote
3
replies
1.4k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 2.4 years ago by ★ 4.7k • 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
2.5 years ago Lenny186 • 0
0
votes
1
reply
848
views
rtracklayer import only subset of ranges
rtracklayer
updated 2.5 years ago by 4.1k • written 2.5 years ago by ▴ 90
4
votes
5
replies
7.8k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.1 years ago by • 0 • written 2.6 years ago by ▴ 50
0
votes
8
replies
2.5k
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 2.6 years ago by • 0
0
votes
1
reply
1.4k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
1
vote
2
replies
2.1k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.8 years ago vanbelj ▴ 30
0
votes
1
reply
891
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
1
vote
4
replies
1.5k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
3.2 years ago Ge Tan ▴ 20
0
votes
2
replies
2.4k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw rtracklayer Windows http
3.3 years ago • updated 3.2 years ago sla • 0
0
votes
4
replies
1.9k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 3.3 years ago by 16k • written 3.3 years ago by • 0
0
votes
0
replies
801
views
Bug in rtracklayer
rtracklayer
3.3 years ago You • 0
2
votes
4
replies
1.4k
views
default behaviour of import.bw
import.bw rtracklayer
3.3 years ago Yixin • 0
0
votes
2
replies
1.4k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
3.5 years ago Arslan • 0
0
votes
0
replies
804
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
3.5 years ago Charles • 0
2
votes
3
replies
2.2k
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 68k • written 3.8 years ago by • 0
2
votes
3
replies
2.1k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 30
5
votes
5
replies
4.4k
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
5.5k
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
6.1k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.0 years ago by ▴ 150 • written 8.9 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
4.3 years ago David • 0
2
votes
2
replies
1.6k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 10
1
vote
1
reply
2.9k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.9 years ago by ★ 11k • written 4.9 years ago by ▴ 20
7
votes
16
replies
4.2k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 3 months ago by • 0 • written 4.9 years ago by ▴ 120
2
votes
6
replies
2.8k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.4 years ago by ★ 1.1k • written 5.0 years ago by ▴ 10
0
votes
1
reply
1.0k
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 5.0 years ago by ★ 11k • written 5.0 years ago by • 0
1
vote
1
reply
869
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
5.3 years ago • updated 5.2 years ago ATpoint ★ 4.7k
1
vote
2
replies
1.1k
views
rtracklayer::export empty score
rtracklayer
updated 5.3 years ago by ★ 11k • written 5.3 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 5.3 years ago by 68k • written 5.3 years ago by ▴ 30
0
votes
0
replies
918
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.3 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 5.6 years ago by ★ 13k • written 5.6 years ago by ▴ 30
0
votes
1
reply
1.2k
views
rtracklayer import bigwig error
rtracklayer
updated 2.1 years ago by ▴ 20 • written 5.6 years ago by ▴ 100
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
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Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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