Showing : rtracklayer • reset
28
votes
25
replies
6.4k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 7.5 years ago by ▴ 10 • written 7.9 years ago by ▴ 100
6
votes
7
replies
3.3k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 9.3 years ago by ★ 1.6k • written 9.7 years ago by ▴ 140
2
votes
8
replies
4.5k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.6 years ago by • 0 • written 7.7 years ago by ▴ 10
3
votes
6
replies
2.2k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by • 0
0
votes
4
replies
1.8k
views
Get genomic sequences
biomaRt rtracklayer biomaRt rtracklayer
updated 15.0 years ago by ▴ 970 • written 15.0 years ago by ▴ 50
0
votes
14
replies
2.9k
views
Genome Browser and R
rtracklayer rtracklayer
11.2 years ago khadeeja ismail ▴ 400
5
votes
3
replies
2.4k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
9.9 years ago • updated 9.8 years ago Thomas Girke ★ 1.7k
3
votes
9
replies
2.6k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 8.9 years ago by ▴ 30 • written 9.0 years ago by ▴ 30
0
votes
6
replies
2.1k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO rtracklayer CAMERA chipseq Gviz ChIPSeq GO rtracklayer CAMERA chipseq Gviz
updated 11.7 years ago by ▴ 750 • written 11.7 years ago by ★ 13k
0
votes
4
replies
1.8k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
0
votes
18
replies
3.1k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.9 years ago by • 0
0
votes
3
replies
1.3k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ▴ 20
0
votes
4
replies
1.8k
views
rtracklayer and UCSC
rtracklayer genomes rtracklayer genomes
updated 15.7 years ago by ▴ 620 • written 15.7 years ago by ★ 6.5k
0
votes
4
replies
1.5k
views
rtracklayer 'track' method, a viewLimits parameter?
rtracklayer rtracklayer
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ★ 1.1k
2
votes
4
replies
2.4k
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 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 30
0
votes
2
replies
3.1k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 80
1
vote
2
replies
1.1k
views
rtracklayer demo bug
rtracklayer
6.8 years ago felix.ernst • 0
0
votes
3
replies
2.3k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer browseGenome save file image UCSC
updated 7.9 years ago by ▴ 10 • written 9.8 years ago by ▴ 60
0
votes
2
replies
1.2k
views
rtracklayer redistributes UCSC source without the original license?
rtracklayer
updated 7.9 years ago by ▴ 10 • written 9.1 years ago by • 0
9
votes
38
replies
8.4k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.9 years ago by ▴ 200
9
votes
9
replies
6.0k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.9 years ago by ▴ 140 • written 8.8 years ago by ★ 7.9k
1
vote
2
replies
1.0k
views
The track cannot show in UCSC
rtracklayer
7.3 years ago zhangqshxxzz • 0
0
votes
4
replies
1.7k
views
rtracklayer issue (getTable)
rtracklayer rtracklayer
updated 15.3 years ago by ▴ 620 • written 15.3 years ago by ★ 1.1k
1
vote
3
replies
2.4k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.8 years ago by 16k • written 10.8 years ago by ★ 11k
0
votes
4
replies
436
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
3 months ago Andreas.Herbst • 0
0
votes
3
replies
1.3k
views
svn version of rtracklayer error
rtracklayer rtracklayer
14.2 years ago Michael Dondrup ▴ 550
5
votes
9
replies
4.4k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 7.6 years ago by ★ 1.3k • written 7.6 years ago by ▴ 10
0
votes
3
replies
1.3k
views
problem about using 'rtracklayer' package to retrieve SNP chromosome position
rtracklayer rtracklayer
updated 15.5 years ago by ▴ 620 • written 15.5 years ago by ▴ 450
0
votes
5
replies
2.5k
views
bigBed support in rtracklayer
rtracklayer rtracklayer
updated 8.6 years ago by ▴ 30 • written 12.1 years ago by ★ 4.2k
0
votes
3
replies
3.7k
views
UCSC: convert from hg18 to hg19 - rtracklayer?
rtracklayer rtracklayer
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ★ 1.1k
0
votes
5
replies
1.9k
views
How to plot microRNA chromosome location
miRNA ideogram GenomeGraphs rtracklayer microRNA miRNA ideogram GenomeGraphs rtracklayer
updated 16.2 years ago by ▴ 40 • written 16.2 years ago by ▴ 620
0
votes
8
replies
3.6k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 740
0
votes
7
replies
1.7k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 13.2 years ago by ★ 11k • written 13.2 years ago by ▴ 190
0
votes
3
replies
3.5k
views
Trying to use the liftOver function from the rtracklayer package in R 2.14.0
PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter
updated 13.1 years ago by ★ 11k • written 13.1 years ago by ★ 1.1k
0
votes
6
replies
2.3k
views
Advice on reading big BED/BAM and ChIP-seq quality control
GO rtracklayer Rsamtools GO rtracklayer Rsamtools
updated 11.7 years ago by ▴ 350 • written 11.7 years ago by ▴ 240
1
vote
4
replies
1.5k
views
[BUG report] rtracklayer cannot handle whitespaces in file names
software error rtracklayer
updated 9.4 years ago by ★ 11k • written 9.4 years ago by ▴ 40
8
votes
5
replies
2.9k
views
import wig to coverage
rtracklayer granges import.wig
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 140
0
votes
2
replies
1.0k
views
rtracklayer colorByStrand - is it possible to add quotes?
rtracklayer
6.8 years ago Janet Young ▴ 740
1
vote
3
replies
1.6k
views
NAs values when importing BED file using import function
rtracklayer NA BED getseq
9.2 years ago Dimitris Polychronopoulos ▴ 80
1
vote
2
replies
1.5k
views
Can I use rtracklayer to get the sequence surrounding a set of variants?
rtracklayer sequencing reference genome
9.4 years ago Stephanie M. Gogarten ▴ 890
0
votes
5
replies
1.9k
views
BED15 format for rtracklayer
Microarray Visualization rtracklayer Microarray Visualization rtracklayer
updated 15.5 years ago by ▴ 620 • written 15.5 years ago by ▴ 500
0
votes
1
reply
1.0k
views
rtracklayer <-> UCSC interaction currently broken
PROcess rtracklayer PROcess rtracklayer
15.6 years ago • updated 15.5 years ago Michael Lawrence ▴ 620
0
votes
1
reply
1.2k
views
rtracklayer and gene symbols
rtracklayer rtracklayer
updated 15.5 years ago by 67k • written 15.5 years ago by ▴ 170
0
votes
1
reply
1.1k
views
Using rtracklayer for ranges of Genomic DNA
rtracklayer rtracklayer
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ▴ 30
0
votes
2
replies
819
views
rtracklayer 'track' method, a viewLimits parameter?
rtracklayer IRanges rtracklayer IRanges
updated 14.2 years ago by ★ 11k • written 14.2 years ago by ★ 1.1k
0
votes
2
replies
1.1k
views
rtracklayer no longer uses TrackSet?
rtracklayer rtracklayer
updated 15.6 years ago by ▴ 620 • written 15.6 years ago by ★ 1.1k
0
votes
2
replies
1.4k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage rtracklayer IRanges Coverage rtracklayer IRanges
updated 15.6 years ago by ★ 1.6k • written 15.6 years ago by ▴ 150
2
votes
2
replies
1.5k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 10
0
votes
6
replies
1.7k
views
rtracklayer: Problems running vignette
rtracklayer rtracklayer
updated 15.6 years ago by ▴ 620 • written 15.6 years ago by ▴ 150
0
votes
1
reply
1.0k
views
rtracklayer 1.6: invalid class "ucscCart" object
hgu133plus2 rtracklayer hgu133plus2 rtracklayer
updated 14.8 years ago by ★ 11k • written 14.8 years ago by ★ 1.1k
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
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Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
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A: Linear regression in DESeq2
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Answer: Differential variability modelling with vst() expression
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