Showing : rtracklayer • reset
0
votes
5
replies
690
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 3 months ago by • 0
0
votes
4
replies
544
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
5 months ago Andreas.Herbst • 0
1
vote
2
replies
604
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
12 months ago thomas • 0
0
votes
4
replies
1.6k
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
2
votes
7
replies
1.0k
views
distanceToNearest
rtracklayer ranges distanceToNearest
14 months ago robjohn70000 • 0
1
vote
0
replies
837
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
16 months ago yujin ▴ 10
1
vote
3
replies
939
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 16 months ago by 16k • written 16 months ago by ▴ 10
1
vote
1
reply
1.0k
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 17 months ago by 16k • written 17 months ago by ▴ 10
0
votes
0
replies
1.2k
views
Problem with loading rtracklayer
rtracklayer
updated 2.1 years ago by 4.1k • written 2.1 years ago by • 0
0
votes
0
replies
688
views
rtracklayer ignores ranges argument
rtracklayer
2.1 years ago Kyle • 0
0
votes
0
replies
907
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.2 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 2.3 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 2.5 years ago by ★ 4.7k • written 2.5 years ago by ▴ 30
2
votes
2
replies
1.1k
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
2.6 years ago • updated 2.5 years ago Lenny186 • 0
0
votes
1
reply
869
views
rtracklayer import only subset of ranges
rtracklayer
updated 2.6 years ago by 4.1k • written 2.6 years ago by ▴ 90
4
votes
5
replies
8.0k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.2 years ago by • 0 • written 2.6 years ago by ▴ 50
0
votes
8
replies
2.6k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.4 years ago by • 0 • written 2.7 years ago by • 0
0
votes
1
reply
1.4k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
1
vote
2
replies
2.1k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.9 years ago vanbelj ▴ 30
0
votes
1
reply
911
views
Rtracklayer
rtracklayer RNASeq gff
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
1
vote
4
replies
1.5k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
3.3 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 sla • 0
0
votes
0
replies
831
views
Bug in rtracklayer
rtracklayer
3.3 years ago You • 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 3.4 years ago by • 0
2
votes
4
replies
1.5k
views
default behaviour of import.bw
import.bw rtracklayer
3.4 years ago • updated 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
820
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
3.5 years ago Charles • 0
2
votes
3
replies
2.3k
views
Importing a bed file
rtracklayer
3.8 years ago Skylar • 0
0
votes
1
reply
1.4k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
0
votes
18
replies
3.3k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 4.0 years ago by • 0
2
votes
3
replies
2.1k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 30
5
votes
5
replies
4.5k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.1 years ago by 4.1k • written 4.2 years ago by ▴ 840
1
vote
5
replies
5.7k
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 4.3 years ago by ★ 11k • written 4.3 years ago by • 0
2
votes
0
replies
1.3k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
4.3 years ago Mikhail Dozmorov ▴ 30
0
votes
0
replies
1.0k
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.4 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
4.3k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4 months ago by • 0 • written 5.0 years ago by ▴ 120
2
votes
6
replies
2.9k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.5 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
891
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 5.1 years ago by ★ 11k • written 5.1 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 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 5.4 years ago by 68k • written 5.4 years ago by ▴ 30
0
votes
0
replies
930
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.4 years ago jovel_juan ▴ 30
2
votes
3
replies
1.9k
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 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 30
0
votes
1
reply
1.2k
views
rtracklayer import bigwig error
rtracklayer
updated 2.2 years ago by ▴ 20 • written 5.7 years ago by ▴ 100
0
votes
1
reply
1.4k
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 5.9 years ago by 16k • written 5.9 years ago by ▴ 10
4
votes
1
reply
1.5k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 6.0 years ago by ★ 11k • written 6.0 years ago by ▴ 180
50 results • Page 1 of 1
Recent ...
Replies
Answer: affy::rma results doesn't match with ncbi website by ATpoint ★ 4.7k
Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…
Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
Awards • All
Popular Question to igor ▴ 50
Popular Question to xiaofeiwang198266 • 0
Scholar to shepherl 4.1k
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 52k
Locations • All
Iran, 43 minutes ago
Japan, 1 hour ago
The city by the bay, 1 hour ago
United States, 1 hour ago
Canada, 1 hour ago
Traffic: 615 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6