Showing : rtracklayer • reset
0
votes
5
replies
596
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 5 weeks ago by • 0
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 8 weeks ago by • 0 • written 4.8 years ago by ▴ 120
0
votes
4
replies
436
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
3 months ago Andreas.Herbst • 0
0
votes
18
replies
3.1k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.9 years ago by • 0
1
vote
2
replies
553
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 10 months ago by 4.1k • written 10 months ago by • 0
9
votes
38
replies
8.4k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.9 years ago by ▴ 200
2
votes
7
replies
976
views
distanceToNearest
rtracklayer ranges distanceToNearest
12 months ago robjohn70000 • 0
1
vote
3
replies
875
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 14 months ago by 16k • written 14 months ago by ▴ 10
1
vote
0
replies
769
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
14 months ago yujin ▴ 10
1
vote
1
reply
947
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 15 months ago by 16k • written 15 months ago by ▴ 10
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
653
views
rtracklayer ignores ranges argument
rtracklayer
23 months ago Kyle • 0
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 24 months ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
0
replies
862
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
24 months ago Delta._.43 ▴ 20
0
votes
1
reply
1.2k
views
rtracklayer import bigwig error
rtracklayer
updated 24 months ago by ▴ 20 • written 5.5 years ago by ▴ 100
4
votes
5
replies
7.4k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.0 years ago by • 0 • written 2.5 years ago by ▴ 50
3
votes
4
replies
1.6k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
2.2 years ago L ▴ 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 2.2 years ago by • 0 • written 2.5 years ago by • 0
1
vote
3
replies
1.3k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 2.3 years ago by ★ 4.6k • written 2.3 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
820
views
rtracklayer import only subset of ranges
rtracklayer
updated 2.4 years ago by 4.1k • written 2.4 years ago by ▴ 90
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
2
votes
4
replies
7.0k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 2.6 years ago by • 0 • written 9.5 years ago by ▴ 90
1
vote
2
replies
2.0k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.7 years ago vanbelj ▴ 30
0
votes
1
reply
867
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
5
votes
5
replies
4.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.9 years ago by 4.1k • written 4.0 years ago by ▴ 840
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 • updated 3.1 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
2
votes
4
replies
1.4k
views
default behaviour of import.bw
import.bw rtracklayer
3.2 years ago Yixin • 0
0
votes
0
replies
775
views
Bug in rtracklayer
rtracklayer
3.2 years ago You • 0
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
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
780
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
3.6 years ago Skylar • 0
0
votes
1
reply
1.3k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.7 years ago by 67k • written 3.7 years ago by • 0
2
votes
3
replies
2.0k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 3.9 years ago by 67k • written 3.9 years ago by ▴ 30
9
votes
9
replies
6.0k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.9 years ago by ▴ 140 • written 8.8 years ago by ★ 7.9k
1
vote
4
replies
3.0k
views
Import Chain - Cannot Import Chain File
rtracklayer
updated 4.1 years ago by ▴ 20 • written 6.4 years ago by • 0
1
vote
5
replies
5.3k
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 4.1 years ago by ★ 11k • written 4.1 years ago by • 0
2
votes
0
replies
1.3k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
4.1 years ago Mikhail Dozmorov ▴ 30
0
votes
0
replies
990
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
1.5k
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
0
votes
1
reply
986
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
820
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 4.9 years ago by ★ 11k • written 4.9 years ago by • 0
0
votes
0
replies
1.3k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
5.2 years ago • updated 5.1 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
50 results • Page 1 of 1
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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
Votes
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
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