Showing : rtracklayer • reset
28
votes
25
replies
5.9k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 6.8 years ago by ▴ 10 • written 7.3 years ago by ▴ 100
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
2
votes
8
replies
4.0k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.0 years ago by • 0 • written 7.0 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 6.0 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 14.4 years ago by ▴ 970 • written 14.4 years ago by ▴ 50
0
votes
14
replies
2.5k
views
Genome Browser and R
rtracklayer rtracklayer
10.6 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 7.0 years ago by ★ 1.3k • written 7.0 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
1.2k
views
svn version of rtracklayer error
rtracklayer rtracklayer
13.6 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
2.3k
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
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
903
views
rtracklayer demo bug
rtracklayer
6.2 years ago felix.ernst • 0
0
votes
3
replies
2.0k
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
6.8k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.3 years ago by ▴ 190
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
1
vote
2
replies
923
views
The track cannot show in UCSC
rtracklayer
6.6 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 11.1 years ago by ▴ 730 • written 11.1 years ago by ★ 13k
0
votes
18
replies
2.6k
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
1.2k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 13.6 years ago by ★ 11k • written 13.6 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 8.0 years ago by ▴ 30 • written 11.5 years ago by ★ 4.2k
0
votes
4
replies
1.4k
views
rtracklayer 'track' method, a viewLimits parameter?
rtracklayer rtracklayer
updated 13.6 years ago by ★ 11k • written 13.6 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 13.1 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 15.6 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 12.8 years ago by 16k • written 12.8 years ago by ▴ 740
0
votes
7
replies
1.5k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 12.5 years ago by ★ 11k • written 12.5 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 12.5 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 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 40
8
votes
5
replies
2.6k
views
import wig to coverage
rtracklayer granges import.wig
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 140
0
votes
2
replies
896
views
rtracklayer colorByStrand - is it possible to add quotes?
rtracklayer
6.1 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
8.5 years ago Dimitris Polychronopoulos ▴ 80
0
votes
5
replies
1.7k
views
BED15 format for rtracklayer
Microarray Visualization rtracklayer Microarray Visualization rtracklayer
updated 14.8 years ago by ▴ 620 • written 14.8 years ago by ▴ 500
0
votes
1
reply
935
views
rtracklayer <-> UCSC interaction currently broken
PROcess rtracklayer PROcess rtracklayer
14.9 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
982
views
Using rtracklayer for ranges of Genomic DNA
rtracklayer rtracklayer
updated 13.6 years ago by ★ 11k • written 13.6 years ago by ▴ 30
0
votes
2
replies
746
views
rtracklayer 'track' method, a viewLimits parameter?
rtracklayer IRanges rtracklayer IRanges
updated 13.6 years ago by ★ 11k • written 13.6 years ago by ★ 1.1k
0
votes
2
replies
955
views
rtracklayer no longer uses TrackSet?
rtracklayer rtracklayer
updated 14.9 years ago by ▴ 620 • written 14.9 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 15.0 years ago by ★ 1.6k • written 15.0 years ago by ▴ 150
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
0
votes
6
replies
1.5k
views
rtracklayer: Problems running vignette
rtracklayer rtracklayer
updated 15.0 years ago by ▴ 620 • written 15.0 years ago by ▴ 150
0
votes
1
reply
931
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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Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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