Showing : rtracklayer • reset
28
votes
25
replies
5.9k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 6.9 years ago by ▴ 10 • written 7.3 years ago by ▴ 100
9
votes
9
replies
5.4k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.3 years ago by ▴ 120 • written 8.1 years ago by ★ 7.9k
9
votes
38
replies
6.9k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.3 years ago by ▴ 190
8
votes
5
replies
2.7k
views
import wig to coverage
rtracklayer granges import.wig
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 140
7
votes
13
replies
2.6k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4.2 years ago by ★ 3.3k • written 4.2 years ago by ▴ 110
6
votes
7
replies
3.0k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 8.7 years ago by ★ 1.6k • written 9.0 years ago by ▴ 140
5
votes
3
replies
2.2k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
9.3 years ago • updated 9.1 years ago Thomas Girke ★ 1.7k
5
votes
9
replies
3.9k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 7.0 years ago by ★ 1.3k • written 7.0 years ago by ▴ 10
5
votes
5
replies
3.3k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.3 years ago by 3.9k • written 3.4 years ago by ▴ 830
4
votes
2
replies
1.0k
views
rtracklayer: how to view coordinates that failed liftover?
rtracklayer
updated 7.4 years ago by ★ 11k • written 7.4 years ago by ▴ 30
4
votes
9
replies
4.4k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
8.1 years ago Leonardo Collado Torres ★ 1.1k
4
votes
2
replies
902
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 50
4
votes
5
replies
5.7k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 16 months ago by • 0 • written 22 months ago by ▴ 50
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 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 180
3
votes
15
replies
3.0k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ★ 1.5k
3
votes
4
replies
1.2k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
18 months ago L ▴ 50
3
votes
2
replies
1.1k
views
Import gff from character?
rtracklayer gff gtf import import.gff3
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 20
3
votes
2
replies
4.3k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 250
3
votes
4
replies
1.9k
views
rtracklayer import.gff3 function no longer working in R 3.4
rtracklayer import.gff3 gff
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 180
3
votes
2
replies
980
views
does import.bw with the selection argument take into account strand?
rtracklayer import.bw
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 180
3
votes
3
replies
1.4k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 5.3 years ago by ★ 11k • written 5.3 years ago by ▴ 120
3
votes
2
replies
4.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 10
3
votes
6
replies
1.9k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by • 0
3
votes
9
replies
2.3k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 8.3 years ago by ▴ 30 • written 8.3 years ago by ▴ 30
3
votes
2
replies
947
views
Long elapsed time using `import.gff3` with a toy example
rtracklayer import.gff3
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 20
2
votes
7
replies
546
views
distanceToNearest
rtracklayer ranges distanceToNearest
4 months ago robjohn70000 • 0
2
votes
3
replies
2.9k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 6.8 years ago by ★ 11k • written 6.8 years ago by • 0
2
votes
4
replies
1.4k
views
rtracklayer::import.bed does not close connections.
rtracklayer
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 180
2
votes
2
replies
1.4k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 6.7 years ago by ★ 11k • written 6.7 years ago by ▴ 10
2
votes
4
replies
2.1k
views
possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
genomicfeatures txdb maketxdbfromucsc maketxdbfrombiomart rtracklayer
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 30
2
votes
2
replies
1.3k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 10
2
votes
8
replies
4.1k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.0 years ago by • 0 • written 7.1 years ago by ▴ 10
2
votes
1
reply
844
views
Why export of empty GRanges to GFF fails?
rtracklayer
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 10
2
votes
3
replies
1.6k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 3.3 years ago by 66k • written 3.3 years ago by ▴ 30
2
votes
3
replies
1.7k
views
Importing a bed file
rtracklayer
3.0 years ago Skylar • 0
2
votes
3
replies
1.4k
views
rtracklayer - export.bw bug
bigwig rtracklayer export.bw
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 20
2
votes
0
replies
991
views
How to liftOver Paired BED (bedpe) data
rtracklayer
3.5 years ago Mikhail Dozmorov ▴ 30
2
votes
3
replies
2.4k
views
import.bed fails on bed file with no scores
rtracklayer import bed files
8.1 years ago jmr • 0
2
votes
1
reply
1.2k
views
Strange first_time object in rtracklayer import
rtracklayer bigwig import
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 10
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 4.9 years ago by ★ 13k • written 4.9 years ago by ▴ 30
2
votes
6
replies
2.0k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 2.7 years ago by ★ 1.1k • written 4.2 years ago by ▴ 10
2
votes
1
reply
1.5k
views
rtracklayer BigBed format
ngs rtracklayer bigbed
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ▴ 100
2
votes
8
replies
3.6k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 740
2
votes
1
reply
1.1k
views
Obsolete use of AC_INIT macro
rtracklayer
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 180
2
votes
6
replies
3.0k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 130
2
votes
1
reply
1.3k
views
problem with export() in rtracklayer
rtracklayer export
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ★ 28k
2
votes
10
replies
2.7k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
9.0 years ago andrew.j.skelton73 ▴ 370
2
votes
7
replies
1.2k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 100
2
votes
4
replies
6.0k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 23 months ago by • 0 • written 8.9 years ago by ▴ 90
2
votes
4
replies
1.2k
views
default behaviour of import.bw
import.bw rtracklayer
2.6 years ago • updated 2.5 years ago Yixin • 0
50 results • Page 1 of 1
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Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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