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rtracklayer
•
reset
9
votes
38
replies
10k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 10.0 years ago by
tangming2005
▴ 200
28
votes
25
replies
7.4k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz
rtracklayer
updated 8.5 years ago by
aina.jene
▴ 10 • written 8.9 years ago by
Ramiro Magno
▴ 100
0
votes
18
replies
4.2k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 4.9 years ago by
lea
• 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
rania.alanany
• 0 • written 5.8 years ago by
Biologist
▴ 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
Michael Lawrence
★ 11k • written 8.5 years ago by
Assa Yeroslaviz
★ 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
Steve Lianoglou
★ 13k • written 15.9 years ago by
sabrina.shao
▴ 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
Michael Lawrence
★ 11k • written 7.4 years ago by
Nicolas Servant
▴ 260
1
vote
10
replies
2.9k
views
UCSC web service API
txdb.hsapiens.ucsc.hg19.knowngene
rtracklayer
updated 9.5 years ago by
Martin Morgan
25k • written 9.5 years ago by
Asma rabe
▴ 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
merv
▴ 150 • written 9.8 years ago by
Ryan C. Thompson
★ 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
Ou, Jianhong
★ 1.3k • written 8.7 years ago by
crysis405
▴ 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
laurent.lacroix
▴ 30 • written 10.0 years ago by
koneill
▴ 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
Michael Lawrence
★ 11k • written 9.6 years ago by
Peter Hickey
▴ 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
Ruoyun
• 0 • written 3.5 years ago by
bonob
• 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
nilan666
• 0 • written 8.7 years ago by
juan-pablo.cerapio-arroyo
▴ 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
Hervé Pagès
16k • written 14.4 years ago by
Janet Young
▴ 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
Michael Lawrence
★ 11k • written 6.9 years ago by
foehn
▴ 100
0
votes
7
replies
2.0k
views
export Views of Rle in rtracklayer
Coverage
rtracklayer
Coverage
rtracklayer
updated 14.2 years ago by
Michael Lawrence
★ 11k • written 14.2 years ago by
jason0701
▴ 190
0
votes
7
replies
2.2k
views
read gz compressed wig files?
Cancer
rtracklayer
Cancer
rtracklayer
updated 14.8 years ago by
Steve Lianoglou
★ 13k • written 14.8 years ago by
Hamid Bolouri
▴ 50
0
votes
7
replies
2.0k
views
rtracklayer cannot export empty BED file
rtracklayer
bed
genomicranges
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
foehn
▴ 100
6
votes
7
replies
3.7k
views
Error: Failed to set session genome to...
gviz
rtracklayer
updated 10.4 years ago by
florian.hahne@novartis.com
★ 1.6k • written 10.7 years ago by
liz.ingsimmons
▴ 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
Michael Stadler
▴ 350 • written 12.7 years ago by
Hari Easwaran
▴ 240
1
vote
6
replies
2.2k
views
"rtracklayer" compilation error
rtracklayer
updated 9.6 years ago by
Mike Smith
★ 6.6k • written 9.6 years ago by
Biologist
▴ 120
0
votes
6
replies
2.6k
views
rtracklayer issue: Tracks don't show up
rtracklayer
bug
session
updated 10.8 years ago by
Michael Lawrence
★ 11k • written 10.8 years ago by
chrarnold
• 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
Robert Ivanek
▴ 750 • written 12.8 years ago by
Guest User
★ 13k
0
votes
6
replies
2.0k
views
load failed for 'Rlibstree'
hgu133plus2
rtracklayer
hgu133plus2
rtracklayer
updated 15.8 years ago by
Seth Falcon
★ 7.4k • written 15.8 years ago by
Paul Shannon
★ 1.1k
0
votes
6
replies
1.5k
views
rtracklayer laying a track
rtracklayer
rtracklayer
updated 14.0 years ago by
Michael Lawrence
★ 11k • written 14.0 years ago by
Guest User
★ 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
Leonardo Collado Torres
★ 1.1k • written 5.9 years ago by
mzwanelen
▴ 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
max
▴ 10 • written 7.7 years ago by
chrisamiller
• 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
Michael Lawrence
★ 11k • written 8.1 years ago by
ssabri
▴ 20
0
votes
6
replies
2.1k
views
GenomicFeatures: makeTranscriptDbFromUCSC on "refGene" supported?
rtracklayer
GenomicFeatures
rtracklayer
GenomicFeatures
updated 15.5 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.5 years ago by
Erik van den Akker
▴ 50
0
votes
6
replies
2.0k
views
rtracklayer: Problems running vignette
rtracklayer
rtracklayer
updated 16.6 years ago by
Michael Lawrence
▴ 620 • written 16.6 years ago by
Simon Anders
▴ 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
Michael Lawrence
★ 11k • written 10.1 years ago by
Darya Vanichkina
▴ 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
Michael Lawrence
★ 11k • written 10.7 years ago by
d r
▴ 150
0
votes
5
replies
2.2k
views
BED15 format for rtracklayer
Microarray
Visualization
rtracklayer
Microarray
Visualization
rtracklayer
updated 16.5 years ago by
Michael Lawrence
▴ 620 • written 16.5 years ago by
rcaloger
▴ 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
Martin Morgan
25k • written 10.7 years ago by
krijgerp
• 0
0
votes
5
replies
1.1k
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 13 months ago by
Aichatou
• 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
shepherl
4.3k • written 5.0 years ago by
svlachavas
▴ 840
0
votes
5
replies
2.9k
views
bigBed support in rtracklayer
rtracklayer
rtracklayer
updated 9.6 years ago by
koneill
▴ 30 • written 13.1 years ago by
Tim Triche
★ 4.2k
0
votes
5
replies
1.7k
views
rtracklayer export fails
rtracklayer
rtracklayer
updated 14.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 14.9 years ago by
Michael Dondrup
▴ 550
8
votes
5
replies
3.3k
views
import wig to coverage
rtracklayer
granges
import.wig
updated 11.0 years ago by
Hervé Pagès
16k • written 11.0 years ago by
liz.ingsimmons
▴ 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
Valerie Obenchain
★ 6.8k • written 12.4 years ago by
Sam McInturf
▴ 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
Camper Chih-Wei Liu
▴ 40 • written 17.2 years ago by
Michael Lawrence
▴ 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
Michael Lawrence
★ 11k • written 5.1 years ago by
Søren
• 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
Walters
• 0 • written 3.5 years ago by
L
▴ 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
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