Showing : rtracklayer • reset
28
votes
25
replies
5.8k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 6.8 years ago by ▴ 10 • written 7.2 years ago by ▴ 100
6
votes
7
replies
2.9k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 8.6 years ago by ★ 1.6k • written 8.9 years ago by ▴ 140
2
votes
8
replies
4.0k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 6.9 years ago by • 0 • written 7.0 years ago by ▴ 10
3
votes
6
replies
1.8k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 6.0 years ago by ▴ 10 • written 6.0 years ago by • 0
0
votes
4
replies
1.6k
views
Get genomic sequences
biomaRt rtracklayer biomaRt rtracklayer
updated 14.3 years ago by ▴ 970 • written 14.3 years ago by ▴ 50
0
votes
14
replies
2.5k
views
Genome Browser and R
rtracklayer rtracklayer
10.5 years ago khadeeja ismail ▴ 400
5
votes
3
replies
2.2k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
9.2 years ago • updated 9.1 years ago Thomas Girke ★ 1.7k
0
votes
4
replies
1.5k
views
rtracklayer and UCSC
rtracklayer genomes rtracklayer genomes
updated 15.0 years ago by ▴ 620 • written 15.0 years ago by ★ 6.5k
5
votes
9
replies
3.8k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Can I use rtracklayer to get the sequence surrounding a set of variants?
rtracklayer sequencing reference genome
8.7 years ago Stephanie M. Gogarten ▴ 870
0
votes
4
replies
1.4k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
0
votes
3
replies
1.1k
views
svn version of rtracklayer error
rtracklayer rtracklayer
13.5 years ago Michael Dondrup ▴ 550
0
votes
3
replies
1.1k
views
problem about using 'rtracklayer' package to retrieve SNP chromosome position
rtracklayer rtracklayer
updated 14.8 years ago by ▴ 620 • written 14.8 years ago by ▴ 450
3
votes
9
replies
2.2k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 8.2 years ago by ▴ 30 • written 8.2 years ago by ▴ 30
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 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 30
0
votes
2
replies
2.8k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 8.2 years ago by ★ 11k • written 8.2 years ago by ▴ 80
1
vote
2
replies
884
views
rtracklayer demo bug
rtracklayer
6.1 years ago felix.ernst • 0
0
votes
3
replies
1.9k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer browseGenome save file image UCSC
updated 7.2 years ago by ▴ 10 • written 9.1 years ago by ▴ 60
0
votes
2
replies
1.1k
views
rtracklayer redistributes UCSC source without the original license?
rtracklayer
updated 7.2 years ago by ▴ 10 • written 8.4 years ago by • 0
9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.2 years ago by ▴ 190
9
votes
9
replies
5.4k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.2 years ago by ▴ 120 • written 8.1 years ago by ★ 7.9k
1
vote
2
replies
917
views
The track cannot show in UCSC
rtracklayer
6.6 years ago • updated 6.5 years ago zhangqshxxzz • 0
0
votes
6
replies
1.9k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO rtracklayer CAMERA chipseq Gviz ChIPSeq GO rtracklayer CAMERA chipseq Gviz
updated 11.0 years ago by ▴ 730 • written 11.0 years ago by ★ 13k
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
0
votes
4
replies
1.5k
views
rtracklayer issue (getTable)
rtracklayer rtracklayer
updated 14.6 years ago by ▴ 620 • written 14.6 years ago by ★ 1.1k
0
votes
3
replies
1.1k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ▴ 20
1
vote
3
replies
2.2k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.1 years ago by 16k • written 10.1 years ago by ★ 11k
0
votes
5
replies
2.3k
views
bigBed support in rtracklayer
rtracklayer rtracklayer
updated 7.9 years ago by ▴ 30 • written 11.4 years ago by ★ 4.2k
0
votes
4
replies
1.3k
views
rtracklayer 'track' method, a viewLimits parameter?
rtracklayer rtracklayer
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ★ 1.1k
0
votes
3
replies
3.5k
views
UCSC: convert from hg18 to hg19 - rtracklayer?
rtracklayer rtracklayer
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ★ 1.1k
0
votes
5
replies
1.7k
views
How to plot microRNA chromosome location
miRNA ideogram GenomeGraphs rtracklayer microRNA miRNA ideogram GenomeGraphs rtracklayer
updated 15.5 years ago by ▴ 40 • written 15.5 years ago by ▴ 620
0
votes
8
replies
3.4k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 12.7 years ago by 16k • written 12.7 years ago by ▴ 740
0
votes
7
replies
1.4k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 190
0
votes
3
replies
3.3k
views
Trying to use the liftOver function from the rtracklayer package in R 2.14.0
PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ★ 1.0k
0
votes
6
replies
2.0k
views
Advice on reading big BED/BAM and ChIP-seq quality control
GO rtracklayer Rsamtools GO rtracklayer Rsamtools
updated 11.0 years ago by ▴ 350 • written 11.0 years ago by ▴ 240
1
vote
4
replies
1.3k
views
[BUG report] rtracklayer cannot handle whitespaces in file names
software error rtracklayer
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 40
8
votes
5
replies
2.6k
views
import wig to coverage
rtracklayer granges import.wig
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 140
0
votes
2
replies
885
views
rtracklayer colorByStrand - is it possible to add quotes?
rtracklayer
6.1 years ago • updated 6.0 years ago Janet Young ▴ 740
1
vote
3
replies
1.4k
views
NAs values when importing BED file using import function
rtracklayer NA BED getseq
8.4 years ago Dimitris Polychronopoulos ▴ 80
0
votes
5
replies
1.6k
views
BED15 format for rtracklayer
Microarray Visualization rtracklayer Microarray Visualization rtracklayer
updated 14.7 years ago by ▴ 620 • written 14.7 years ago by ▴ 500
0
votes
1
reply
932
views
rtracklayer <-> UCSC interaction currently broken
PROcess rtracklayer PROcess rtracklayer
14.8 years ago Michael Lawrence ▴ 620
0
votes
1
reply
1.1k
views
rtracklayer and gene symbols
rtracklayer rtracklayer
updated 14.8 years ago by 65k • written 14.8 years ago by ▴ 170
0
votes
1
reply
972
views
Using rtracklayer for ranges of Genomic DNA
rtracklayer rtracklayer
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ▴ 30
0
votes
2
replies
737
views
rtracklayer 'track' method, a viewLimits parameter?
rtracklayer IRanges rtracklayer IRanges
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ★ 1.1k
0
votes
2
replies
943
views
rtracklayer no longer uses TrackSet?
rtracklayer rtracklayer
updated 14.8 years ago by ▴ 620 • written 14.8 years ago by ★ 1.1k
0
votes
2
replies
1.2k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage rtracklayer IRanges Coverage rtracklayer IRanges
updated 14.9 years ago by ★ 1.6k • written 14.9 years ago by ▴ 150
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 10
0
votes
6
replies
1.5k
views
rtracklayer: Problems running vignette
rtracklayer rtracklayer
updated 14.9 years ago by ▴ 620 • written 14.9 years ago by ▴ 150
0
votes
1
reply
925
views
rtracklayer 1.6: invalid class "ucscCart" object
hgu133plus2 rtracklayer hgu133plus2 rtracklayer
updated 14.1 years ago by ★ 11k • written 14.1 years ago by ★ 1.1k
0
votes
6
replies
1.5k
views
load failed for 'Rlibstree'
hgu133plus2 rtracklayer hgu133plus2 rtracklayer
updated 14.1 years ago by ★ 7.4k • written 14.1 years ago by ★ 1.1k
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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