Showing : Ucsc • reset
3
votes
4
replies
409
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
4 months ago L ▴ 50
2
votes
3
replies
1.0k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 3.0 years ago by 62k • written 3.0 years ago by ▴ 80
1
vote
1
reply
2.0k
views
TxDb.Hsapiens.UCSC.hg38.knownGene In install.packages(pkgs = doing, lib = lib, ...) Non-Zero Exit Status
annotation UCSC doing lib mgcv
updated 4.0 years ago by 62k • written 4.0 years ago by • 0
2
votes
4
replies
936
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 4.3 years ago by 62k • written 4.3 years ago by ▴ 10
3
votes
6
replies
1.3k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by • 0
0
votes
6
replies
1.0k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
5.1 years ago • updated 5.0 years ago dusan.petrovic • 0
0
votes
2
replies
838
views
How to get UCSC url when use rtracklayer, contain the track in the url ,it may be very useful
rtracklayer UCSC ucsctrack
updated 5.3 years ago by 62k • written 5.3 years ago by • 0
0
votes
1
reply
736
views
Gviz error in IdeogramTrack command
Gviz ucsc
5.4 years ago Taiki Tsutsui • 0
1
vote
4
replies
737
views
Simple UCSC to transcript annotation
annotation ucsc tdx transcripts
5.7 years ago AntonS • 0
0
votes
2
replies
941
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 5.7 years ago by ★ 6.7k • written 5.7 years ago by • 0
3
votes
4
replies
1.0k
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 5.7 years ago by ★ 6.7k • written 5.8 years ago by • 0
0
votes
3
replies
1.5k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer browseGenome save file image UCSC
updated 6.1 years ago by ▴ 10 • written 8.0 years ago by ▴ 60
1
vote
4
replies
1.9k
views
Giemsa stain annotation/nomenclature for UCSC cytoband tracks
ucsc ucsctrack ggbio Gviz hg19
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by ▴ 10
0
votes
0
replies
966
views
Error IdeoViz package: getIdeo
IdeoViz UCSC download_error
6.1 years ago kaleb.gatto • 0
0
votes
5
replies
2.4k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer mm9 ucsc
updated 6.7 years ago by 25k • written 7.9 years ago by • 0
2
votes
32
replies
3.4k
views
Gviz error 'Expectation Failed'
gviz ucsc
6.8 years ago • updated 6.7 years ago Tom ▴ 10
2
votes
3
replies
2.1k
views
Loading BSgenome.Hsapiens.UCSC.hg19 package
ucsc bsgenome.hsapiens.ucsc.hg19
updated 7.0 years ago by 25k • written 7.0 years ago by • 0
0
votes
1
reply
1.1k
views
Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
gviz ucsc
updated 7.1 years ago by ▴ 730 • written 7.1 years ago by • 0
3
votes
5
replies
1.3k
views
UcscTrack and BED without headers
gviz BED Ucsc UcscTrack
7.2 years ago Andy91 ▴ 60
1
vote
4
replies
2.1k
views
It is possible to use Gviz without a valid UCSC genome?
gviz UCSC
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by ▴ 40
1
vote
2
replies
2.9k
views
Converting annotation from UCSC to Ensembl
ensembl ucsc annotation
updated 7.3 years ago by 62k • written 7.3 years ago by ▴ 110
2
votes
2
replies
1.9k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter granges refseq ucsc organismdb
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 10
2
votes
10
replies
2.1k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
7.8 years ago andrew.j.skelton73 ▴ 360
0
votes
1
reply
1.4k
views
Using European UCSC server in Gviz
Gviz UCSC
updated 7.8 years ago by ★ 1.6k • written 7.9 years ago by • 0
2
votes
2
replies
1.3k
views
UCSC Genome, match accession (NM_#####) with actual gene name
ucsc gene set analysis genome annotation
updated 7.9 years ago by 62k • written 7.9 years ago by • 0
0
votes
2
replies
1.3k
views
Show the name of genetic elements and change the color according to its feature using UcscTrack
gviz ucsc
8.1 years ago • updated 8.0 years ago Tiphaine Martin ▴ 40
0
votes
1
reply
1.1k
views
Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures genomicranges ucsc
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 90
27 results • Page 1 of 1
Recent ...
Replies
Comment: How to extract proteins from PCs in plot_pca in DEP package by Basti ▴ 700
Which information do you want precisely ? plot_pca is just a wrapper for PCA visualization, but it applies prcomp to perform PCA : https://…
Comment: [limma::kegga] Pathway names all NA by Gordon Smyth 47k
The reason why installing limma didn't solve the problem was because you were using Bioconductor 3.15 rather than the current release, whic…
Comment: [limma::kegga] Pathway names all NA by andrewsm • 0
Thank you Gordon for the quick response. I saw something along those lines in the NEWS notes so did try ```{r} BiocManager:install("limma"…
Comment: Time-course, comparison of two groups by Gordon Smyth 47k
With 4 time points there are 3 df between time points, so your spline analysis with `df=3` is exactly the same as if you had treated time a…
Comment: Does DiffBind make consensus peaks sets for samples from a given condition (e.g. by tahir.msajid • 0
Hi Rory, I am normalizing the counts with the following options: `normalized <- dba.normalize(counts, method=DBA_DESEQ2, normalize = DBA_N…
Votes
Comment: Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Are polynomial contrasts for a time factor possible in DESeq2?
Are polynomial contrasts for a time factor possible in DESeq2?
Answer: How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_R
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