Showing : rtracklayer • reset
0
votes
5
replies
596
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 4 weeks ago by • 0
0
votes
4
replies
436
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
3 months ago Andreas.Herbst • 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
2
votes
7
replies
975
views
distanceToNearest
rtracklayer ranges distanceToNearest
12 months ago robjohn70000 • 0
1
vote
0
replies
769
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
14 months ago yujin ▴ 10
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
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
0
votes
0
replies
862
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
24 months 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 24 months ago by • 0 • written 2.2 years ago by ▴ 10
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
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
819
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
7.4k
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
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
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
2.7 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
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
0
replies
775
views
Bug in rtracklayer
rtracklayer
3.2 years ago You • 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
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
0
votes
18
replies
3.1k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.9 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
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
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
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
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
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
0
votes
0
replies
890
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 24 months ago by ▴ 20 • written 5.5 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 5.7 years ago by 16k • written 5.7 years ago by ▴ 10
4
votes
1
reply
1.4k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 5.8 years ago by ★ 11k • written 5.9 years ago by ▴ 180
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…
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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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