Showing : rtracklayer • reset
1
vote
2
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238
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
6 weeks ago thomas • 0
0
votes
4
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299
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
9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.2 years ago by ▴ 190
2
votes
7
replies
479
views
distanceToNearest
rtracklayer ranges distanceToNearest
3 months ago robjohn70000 • 0
1
vote
0
replies
427
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
5 months ago yujin ▴ 10
1
vote
3
replies
587
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
453
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 6 months ago by 16k • written 6 months ago by ▴ 10
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.1 years ago by • 0
0
votes
0
replies
697
views
Problem with loading rtracklayer
rtracklayer
updated 14 months ago by 3.8k • written 14 months ago by • 0
0
votes
0
replies
492
views
rtracklayer ignores ranges argument
rtracklayer
14 months ago Kyle • 0
0
votes
0
replies
576
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
858
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
754
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
577
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 21 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
943
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 22 months ago by 65k • written 22 months ago by • 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.0 years ago vanbelj ▴ 30
0
votes
1
reply
687
views
Rtracklayer
rtracklayer RNASeq gff
updated 2.1 years ago by 65k • written 2.1 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
4
replies
1.4k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
0
votes
0
replies
541
views
Bug in rtracklayer
rtracklayer
2.5 years ago You • 0
2
votes
4
replies
1.1k
views
default behaviour of import.bw
import.bw rtracklayer
2.5 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
608
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
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
958
views
How to liftOver Paired BED (bedpe) data
rtracklayer
3.4 years ago Mikhail Dozmorov ▴ 30
9
votes
9
replies
5.4k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.2 years ago by ▴ 120 • written 8.1 years ago by ★ 7.9k
0
votes
0
replies
713
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
3.5 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 ★ 3.3k • 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
761
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
630
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
835
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
727
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
904
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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