Showing : rtracklayer • reset
9
votes
38
replies
10k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 10.0 years ago by ▴ 200
28
votes
25
replies
7.4k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 8.5 years ago by ▴ 10 • written 8.9 years ago by ▴ 100
0
votes
18
replies
4.2k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 4.9 years ago by • 0
7
votes
16
replies
5.3k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 14 months ago by • 0 • written 5.8 years ago by ▴ 120
3
votes
15
replies
4.3k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ★ 1.5k
0
votes
14
replies
4.1k
views
Genome Browser and R
rtracklayer rtracklayer
12.3 years ago • updated 12.2 years ago khadeeja ismail ▴ 400
0
votes
12
replies
3.8k
views
how to use rtracklayer to retrieve sequence of list of coordinates
rtracklayer rtracklayer
updated 15.9 years ago by ★ 13k • written 15.9 years ago by ▴ 220
1
vote
12
replies
7.1k
views
Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Centos7.3 R3.5.1 openssl-1.1.1)
software error rtracklayer bioconductor openssl
7.1 years ago ruan_wei_dong • 0
1
vote
10
replies
3.2k
views
rtracklayer export bedGraph cannot be loaded into UCSC
rtracklayer
updated 7.4 years ago by ★ 11k • written 7.4 years ago by ▴ 260
1
vote
10
replies
2.9k
views
UCSC web service API
txdb.hsapiens.ucsc.hg19.knowngene rtracklayer
updated 9.5 years ago by 25k • written 9.5 years ago by ▴ 290
2
votes
10
replies
3.5k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
10.6 years ago andrew.j.skelton73 ▴ 370
4
votes
9
replies
5.9k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
9.7 years ago Leonardo Collado Torres ★ 1.1k
9
votes
9
replies
6.7k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 5.0 years ago by ▴ 150 • written 9.8 years ago by ★ 7.9k
5
votes
9
replies
5.3k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.7 years ago by ★ 1.3k • written 8.7 years ago by ▴ 10
3
votes
9
replies
3.2k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 10.0 years ago by ▴ 30 • written 10.0 years ago by ▴ 30
2
votes
8
replies
4.7k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 760
0
votes
8
replies
3.1k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 3.3 years ago by • 0 • written 3.5 years ago by • 0
2
votes
8
replies
5.1k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 8.7 years ago by • 0 • written 8.7 years ago by ▴ 10
0
votes
8
replies
4.0k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 14.4 years ago by 16k • written 14.4 years ago by ▴ 740
2
votes
7
replies
1.4k
views
distanceToNearest
rtracklayer ranges distanceToNearest
2.0 years ago robjohn70000 • 0
2
votes
7
replies
1.7k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 100
0
votes
7
replies
2.0k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ▴ 190
0
votes
7
replies
2.2k
views
read gz compressed wig files?
Cancer rtracklayer Cancer rtracklayer
updated 14.8 years ago by ★ 13k • written 14.8 years ago by ▴ 50
0
votes
7
replies
2.0k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 100
6
votes
7
replies
3.7k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 10.4 years ago by ★ 1.6k • written 10.7 years ago by ▴ 140
0
votes
6
replies
2.7k
views
Advice on reading big BED/BAM and ChIP-seq quality control
GO rtracklayer Rsamtools GO rtracklayer Rsamtools
updated 12.7 years ago by ▴ 350 • written 12.7 years ago by ▴ 240
1
vote
6
replies
2.2k
views
"rtracklayer" compilation error
rtracklayer
updated 9.6 years ago by ★ 6.6k • written 9.6 years ago by ▴ 120
0
votes
6
replies
2.6k
views
rtracklayer issue: Tracks don't show up
rtracklayer bug session
updated 10.8 years ago by ★ 11k • written 10.8 years ago by • 0
0
votes
6
replies
2.5k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO rtracklayer CAMERA chipseq Gviz ChIPSeq GO rtracklayer CAMERA chipseq Gviz
updated 12.7 years ago by ▴ 750 • written 12.8 years ago by ★ 13k
0
votes
6
replies
2.0k
views
load failed for 'Rlibstree'
hgu133plus2 rtracklayer hgu133plus2 rtracklayer
updated 15.8 years ago by ★ 7.4k • written 15.8 years ago by ★ 1.1k
0
votes
6
replies
1.5k
views
rtracklayer laying a track
rtracklayer rtracklayer
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ★ 13k
2
votes
6
replies
3.5k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 4.3 years ago by ★ 1.1k • written 5.9 years ago by ▴ 10
3
votes
6
replies
2.7k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 7.7 years ago by ▴ 10 • written 7.7 years ago by • 0
0
votes
6
replies
2.8k
views
Add columns to granges object that sum score around range
R Grang r granges rtracklayer
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 20
0
votes
6
replies
2.1k
views
GenomicFeatures: makeTranscriptDbFromUCSC on "refGene" supported?
rtracklayer GenomicFeatures rtracklayer GenomicFeatures
updated 15.5 years ago by 6.7k • written 15.5 years ago by ▴ 50
0
votes
6
replies
2.0k
views
rtracklayer: Problems running vignette
rtracklayer rtracklayer
updated 16.6 years ago by ▴ 620 • written 16.6 years ago by ▴ 150
2
votes
6
replies
3.7k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 130
0
votes
6
replies
3.4k
views
Problem with importing bigwig files generated in galaxy into R
import.bw rtracklayer
updated 10.7 years ago by ★ 11k • written 10.7 years ago by ▴ 150
0
votes
5
replies
2.2k
views
BED15 format for rtracklayer
Microarray Visualization rtracklayer Microarray Visualization rtracklayer
updated 16.5 years ago by ▴ 620 • written 16.5 years ago by ▴ 500
0
votes
5
replies
3.4k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer mm9 ucsc
updated 9.6 years ago by 25k • written 10.7 years ago by • 0
0
votes
5
replies
1.1k
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 13 months ago by • 0
0
votes
5
replies
1.7k
views
rtracklayer error?
Cancer rtracklayer Cancer rtracklayer
12.5 years ago Janet Young ▴ 740
5
votes
5
replies
5.4k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 4.0 years ago by 4.3k • written 5.0 years ago by ▴ 840
0
votes
5
replies
2.9k
views
bigBed support in rtracklayer
rtracklayer rtracklayer
updated 9.6 years ago by ▴ 30 • written 13.1 years ago by ★ 4.2k
0
votes
5
replies
1.7k
views
rtracklayer export fails
rtracklayer rtracklayer
updated 14.9 years ago by 6.7k • written 14.9 years ago by ▴ 550
8
votes
5
replies
3.3k
views
import wig to coverage
rtracklayer granges import.wig
updated 11.0 years ago by 16k • written 11.0 years ago by ▴ 140
0
votes
5
replies
2.2k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 12.4 years ago by ★ 6.8k • written 12.4 years ago by ▴ 300
0
votes
5
replies
2.2k
views
How to plot microRNA chromosome location
miRNA ideogram GenomeGraphs rtracklayer microRNA miRNA ideogram GenomeGraphs rtracklayer
updated 17.2 years ago by ▴ 40 • written 17.2 years ago by ▴ 620
1
vote
5
replies
6.7k
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 5.1 years ago by ★ 11k • written 5.1 years ago by • 0
4
votes
5
replies
9.2k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 3.0 years ago by • 0 • written 3.5 years ago by ▴ 50
262 results • Page 1 of 6
Recent ...
Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
United States, 2 minutes ago
United States, 22 minutes ago
United States, 41 minutes ago
Germany, 45 minutes ago
United States, 1 hour ago
Traffic: 1909 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