Showing : rtracklayer • reset
0
votes
5
replies
866
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 8 months ago by • 0
0
votes
4
replies
736
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
11 months ago Andreas.Herbst • 0
1
vote
2
replies
705
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
18 months ago thomas • 0
0
votes
4
replies
2.0k
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 18 months ago by 4.2k • written 18 months ago by • 0
9
votes
38
replies
9.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 9.6 years ago by ▴ 200
2
votes
7
replies
1.2k
views
distanceToNearest
rtracklayer ranges distanceToNearest
20 months ago • updated 19 months ago robjohn70000 • 0
1
vote
0
replies
937
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
22 months ago yujin ▴ 10
1
vote
3
replies
1.1k
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 22 months ago by 16k • written 22 months ago by ▴ 10
1
vote
1
reply
1.2k
views
rtracklayer error for browserSession UCSC
rtracklayer
updated 22 months ago by 16k • written 22 months ago by ▴ 10
0
votes
18
replies
3.7k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 4.5 years ago by • 0
0
votes
0
replies
1.3k
views
Problem with loading rtracklayer
rtracklayer
updated 2.5 years ago by 4.2k • written 2.5 years ago by • 0
0
votes
0
replies
755
views
rtracklayer ignores ranges argument
rtracklayer
2.6 years ago Kyle • 0
0
votes
0
replies
999
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.6 years ago Delta._.43 ▴ 20
2
votes
3
replies
2.9k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 2.6 years ago by • 0 • written 2.8 years ago by ▴ 10
3
votes
4
replies
2.0k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
2.8 years ago L ▴ 50
1
vote
3
replies
1.6k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 3.0 years ago by ★ 4.9k • written 3.0 years ago by ▴ 30
2
votes
2
replies
1.2k
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
3.0 years ago Lenny186 • 0
0
votes
1
reply
953
views
rtracklayer import only subset of ranges
rtracklayer
updated 3.0 years ago by 4.2k • written 3.0 years ago by ▴ 90
4
votes
5
replies
8.8k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.6 years ago by • 0 • written 3.1 years ago by ▴ 50
0
votes
8
replies
2.8k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.9 years ago by • 0 • written 3.1 years ago by • 0
0
votes
1
reply
1.6k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
1
vote
2
replies
2.3k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.4 years ago vanbelj ▴ 30
0
votes
1
reply
992
views
Rtracklayer
rtracklayer RNASeq gff
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
1
vote
4
replies
1.7k
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
3.7 years ago Ge Tan ▴ 20
0
votes
2
replies
2.6k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw rtracklayer Windows http
3.8 years ago sla • 0
0
votes
4
replies
2.1k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 3.8 years ago by 16k • written 3.8 years ago by • 0
0
votes
0
replies
952
views
Bug in rtracklayer
rtracklayer
3.8 years ago You • 0
2
votes
4
replies
1.6k
views
default behaviour of import.bw
import.bw rtracklayer
3.8 years ago Yixin • 0
0
votes
2
replies
1.5k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
4.0 years ago Arslan • 0
0
votes
0
replies
887
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
4.0 years ago Charles • 0
2
votes
3
replies
2.5k
views
Importing a bed file
rtracklayer
4.3 years ago Skylar • 0
0
votes
1
reply
1.5k
views
Bug in rtracklayer liftOver function
rtracklayer
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
2
votes
3
replies
2.4k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 30
5
votes
5
replies
5.0k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.6 years ago by 4.2k • written 4.7 years ago by ▴ 840
1
vote
5
replies
6.2k
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 4.8 years ago by ★ 11k • written 4.8 years ago by • 0
2
votes
0
replies
1.5k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
4.8 years ago Mikhail Dozmorov ▴ 30
9
votes
9
replies
6.4k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.6 years ago by ▴ 150 • written 9.4 years ago by ★ 7.9k
0
votes
0
replies
1.1k
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.8 years ago David • 0
2
votes
2
replies
1.8k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 10
1
vote
1
reply
3.1k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 20
7
votes
16
replies
4.8k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 9 months ago by • 0 • written 5.5 years ago by ▴ 120
2
votes
6
replies
3.2k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.9 years ago by ★ 1.1k • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 5.5 years ago by ★ 11k • written 5.5 years ago by • 0
1
vote
1
reply
984
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 5.5 years ago by ★ 11k • written 5.6 years ago by • 0
0
votes
0
replies
1.5k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
5.8 years ago ATpoint ★ 4.9k
1
vote
2
replies
1.2k
views
rtracklayer::export empty score
rtracklayer
updated 5.8 years ago by ★ 11k • written 5.8 years ago by • 0
0
votes
4
replies
2.1k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 30
0
votes
0
replies
990
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
5.8 years ago jovel_juan ▴ 30
2
votes
3
replies
2.1k
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 6.1 years ago by ★ 13k • written 6.1 years ago by ▴ 30
0
votes
1
reply
1.3k
views
rtracklayer import bigwig error
rtracklayer
updated 2.6 years ago by ▴ 20 • written 6.2 years ago by ▴ 100
262 results • Page 1 of 6
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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