Showing : rtracklayer • reset
1
vote
2
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231
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
6 weeks ago thomas • 0
0
votes
4
replies
290
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 8 weeks ago by 3.8k • written 8 weeks ago by • 0
2
votes
7
replies
470
views
distanceToNearest
rtracklayer ranges distanceToNearest
3 months ago robjohn70000 • 0
1
vote
0
replies
419
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
5 months ago yujin ▴ 10
1
vote
3
replies
579
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 5 months ago by 16k • written 5 months ago by ▴ 10
1
vote
1
reply
441
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 5 months ago by 16k • written 5 months ago by ▴ 10
0
votes
0
replies
687
views
Problem with loading rtracklayer
rtracklayer
updated 14 months ago by 3.8k • written 14 months ago by • 0
0
votes
0
replies
486
views
rtracklayer ignores ranges argument
rtracklayer
14 months ago Kyle • 0
0
votes
0
replies
566
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
15 months ago Delta._.43 ▴ 20
2
votes
3
replies
1.7k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 15 months ago by • 0 • written 17 months ago by ▴ 10
3
votes
4
replies
1.1k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
17 months ago L ▴ 50
1
vote
3
replies
848
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 19 months ago by ★ 4.0k • written 19 months ago by ▴ 30
2
votes
2
replies
748
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
20 months ago • updated 19 months ago Lenny186 • 0
0
votes
1
reply
570
views
rtracklayer import only subset of ranges
rtracklayer
updated 20 months ago by 3.8k • written 20 months ago by ▴ 90
4
votes
5
replies
5.4k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 15 months ago by • 0 • written 20 months ago by ▴ 50
0
votes
8
replies
1.8k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 18 months ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
933
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 21 months ago by 65k • written 21 months ago by • 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
24 months ago vanbelj ▴ 30
0
votes
1
reply
683
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.0 years ago by 65k • written 2.0 years ago by • 0
1
vote
4
replies
1.1k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
2.4 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
2.4 years ago sla • 0
0
votes
0
replies
539
views
Bug in rtracklayer
rtracklayer
2.4 years ago You • 0
0
votes
4
replies
1.4k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
2
votes
4
replies
1.1k
views
default behaviour of import.bw
import.bw rtracklayer
2.5 years ago • updated 2.4 years ago Yixin • 0
0
votes
2
replies
1.0k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.6 years ago Arslan • 0
0
votes
0
replies
605
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
2.6 years ago Charles • 0
2
votes
3
replies
1.7k
views
Importing a bed file
rtracklayer
2.9 years ago Skylar • 0
0
votes
1
reply
1.1k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.0 years ago by 65k • written 3.0 years ago by • 0
0
votes
21
replies
2.4k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.1 years ago by • 0
2
votes
3
replies
1.6k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
5
votes
5
replies
3.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.2 years ago by 3.8k • written 3.3 years ago by ▴ 830
1
vote
5
replies
3.9k
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 3.4 years ago by ★ 11k • written 3.4 years ago by • 0
2
votes
0
replies
951
views
How to liftOver Paired BED (bedpe) data
rtracklayer
3.4 years ago Mikhail Dozmorov ▴ 30
0
votes
0
replies
709
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
3.4 years ago David • 0
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 10
1
vote
1
reply
2.2k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.0 years ago by ★ 11k • written 4.0 years ago by ▴ 20
7
votes
13
replies
2.5k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4.1 years ago by ★ 3.2k • written 4.1 years ago by ▴ 110
2
votes
6
replies
1.9k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 2.6 years ago by ★ 1.0k • written 4.1 years ago by ▴ 10
0
votes
1
reply
758
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 4.1 years ago by ★ 11k • written 4.1 years ago by • 0
1
vote
1
reply
624
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 4.2 years ago by ★ 11k • written 4.2 years ago by • 0
0
votes
0
replies
1.1k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
4.4 years ago ATpoint ★ 4.0k
1
vote
2
replies
828
views
rtracklayer::export empty score
rtracklayer
updated 4.4 years ago by ★ 11k • written 4.4 years ago by • 0
0
votes
4
replies
1.6k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 30
0
votes
0
replies
721
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
4.5 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 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
0
votes
1
reply
898
views
rtracklayer import bigwig error
rtracklayer
updated 15 months ago by ▴ 20 • written 4.8 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 5.0 years ago by 16k • written 5.0 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 5.1 years ago by ★ 11k • written 5.1 years ago by ▴ 170
2
votes
7
replies
1.2k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 5.1 years ago by ★ 11k • written 5.1 years ago by ▴ 100
0
votes
4
replies
1.1k
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
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Comment: DESeq2 setting significant p-value by Dev • 0
Sir but when I put in the data via the csv file, it was showing the gene names then but now when i set it in the form factor it is not show…
Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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