Showing : UCSC • reset
0
votes
4
replies
553
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
6 months ago Andreas.Herbst • 0
1
vote
0
replies
845
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
17 months ago yujin ▴ 10
3
votes
4
replies
1.7k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
2.4 years ago L ▴ 50
2
votes
3
replies
2.2k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 100
1
vote
1
reply
3.0k
views
TxDb.Hsapiens.UCSC.hg38.knownGene In install.packages(pkgs = doing, lib = lib, ...) Non-Zero Exit Status
annotation UCSC doing lib mgcv
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
2
votes
4
replies
1.8k
views
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
txdb txdb.hsapiens.ucsc.hg19.knowngene granges exons ucsc
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 10
3
votes
6
replies
2.3k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 6.9 years ago by ▴ 10 • written 6.9 years ago by • 0
0
votes
6
replies
1.9k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
7.1 years ago dusan.petrovic • 0
0
votes
2
replies
1.4k
views
How to get UCSC url when use rtracklayer, contain the track in the url ,it may be very useful
rtracklayer UCSC ucsctrack
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
0
votes
1
reply
1.3k
views
Gviz error in IdeogramTrack command
Gviz ucsc
7.4 years ago Taiki Tsutsui ▴ 10
1
vote
4
replies
1.3k
views
Simple UCSC to transcript annotation
annotation ucsc tdx transcripts
7.7 years ago AntonS • 0
0
votes
2
replies
1.7k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 7.7 years ago by ★ 6.8k • written 7.7 years ago by • 0
3
votes
4
replies
1.7k
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 7.8 years ago by ★ 6.8k • written 7.8 years ago by • 0
0
votes
3
replies
2.4k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer browseGenome save file image UCSC
updated 8.1 years ago by ▴ 10 • written 10.0 years ago by ▴ 60
1
vote
4
replies
3.3k
views
Giemsa stain annotation/nomenclature for UCSC cytoband tracks
ucsc ucsctrack ggbio Gviz hg19
updated 8.1 years ago by ▴ 10 • written 8.1 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Error IdeoViz package: getIdeo
IdeoViz UCSC download_error
8.1 years ago kaleb.gatto • 0
0
votes
5
replies
3.2k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer mm9 ucsc
updated 8.7 years ago by 25k • written 9.9 years ago by • 0
2
votes
32
replies
6.0k
views
Gviz error 'Expectation Failed'
gviz ucsc
8.8 years ago • updated 8.7 years ago Tom ▴ 10
2
votes
3
replies
2.7k
views
Loading BSgenome.Hsapiens.UCSC.hg19 package
ucsc bsgenome.hsapiens.ucsc.hg19
updated 9.0 years ago by 25k • written 9.0 years ago by • 0
0
votes
1
reply
1.6k
views
Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
gviz ucsc
updated 9.1 years ago by ▴ 750 • written 9.1 years ago by • 0
3
votes
5
replies
2.0k
views
UcscTrack and BED without headers
gviz BED Ucsc UcscTrack
9.2 years ago Andy91 ▴ 60
1
vote
4
replies
2.9k
views
It is possible to use Gviz without a valid UCSC genome?
gviz UCSC
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by ▴ 40
1
vote
2
replies
3.9k
views
Converting annotation from UCSC to Ensembl
ensembl ucsc annotation
updated 9.3 years ago by 68k • written 9.3 years ago by ▴ 110
2
votes
2
replies
3.3k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter granges refseq ucsc organismdb
updated 9.3 years ago by ★ 3.4k • written 9.3 years ago by ▴ 10
2
votes
10
replies
3.0k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
9.8 years ago andrew.j.skelton73 ▴ 370
0
votes
1
reply
1.8k
views
Using European UCSC server in Gviz
Gviz UCSC
updated 9.8 years ago by ★ 1.6k • written 9.9 years ago by • 0
2
votes
2
replies
1.9k
views
UCSC Genome, match accession (NM_#####) with actual gene name
ucsc gene set analysis genome annotation
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
0
votes
2
replies
1.8k
views
Show the name of genetic elements and change the color according to its feature using UcscTrack
gviz ucsc
10.1 years ago • updated 10.0 years ago Tiphaine Martin ▴ 40
0
votes
1
reply
1.4k
views
Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures genomicranges ucsc
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 90
29 results • Page 1 of 1
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Replies
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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