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Showing :
UCSC
•
reset
0
votes
4
replies
364
views
rtracklayer accessing UCSC data table not working
UCSC
rtracklayer
getTable
9 weeks ago • updated 8 weeks ago
Andreas.Herbst
• 0
1
vote
0
replies
726
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
13 months ago
yujin
▴ 10
3
votes
4
replies
1.6k
views
Convert a bed file to bigBed with rtracklayer
bed
bigBed
rtracklayer
ucsc
2.0 years ago
L
▴ 50
2
votes
3
replies
2.0k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 4.7 years ago by
James W. MacDonald
67k • written 4.7 years ago by
foehn
▴ 100
1
vote
1
reply
2.9k
views
TxDb.Hsapiens.UCSC.hg38.knownGene In install.packages(pkgs = doing, lib = lib, ...) Non-Zero Exit Status
annotation
UCSC
doing
lib
mgcv
updated 5.7 years ago by
James W. MacDonald
67k • written 5.7 years ago by
tdfyoder
• 0
2
votes
4
replies
1.7k
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 6.0 years ago by
James W. MacDonald
67k • written 6.0 years ago by
olavur
▴ 10
3
votes
6
replies
2.1k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer
ucsc
ensgene
updated 6.6 years ago by
max
▴ 10 • written 6.6 years ago by
chrisamiller
• 0
0
votes
6
replies
1.7k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq
methylation
ensembl
ucsc
limma
6.8 years ago • updated 6.7 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 7.0 years ago by
James W. MacDonald
67k • written 7.0 years ago by
zhangqshxxzz
• 0
0
votes
1
reply
1.3k
views
Gviz error in IdeogramTrack command
Gviz
ucsc
7.1 years ago
Taiki Tsutsui
▴ 10
1
vote
4
replies
1.2k
views
Simple UCSC to transcript annotation
annotation
ucsc
tdx
transcripts
7.4 years ago
AntonS
• 0
0
votes
2
replies
1.6k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 7.4 years ago by
Valerie Obenchain
★ 6.8k • written 7.4 years ago by
Lna
• 0
3
votes
4
replies
1.6k
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 7.4 years ago by
Valerie Obenchain
★ 6.8k • written 7.4 years ago by
Lna
• 0
0
votes
3
replies
2.2k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer
browseGenome
save file
image
UCSC
updated 7.8 years ago by
maximilianh
▴ 10 • written 9.6 years ago by
James Perkins
▴ 60
1
vote
4
replies
3.0k
views
Giemsa stain annotation/nomenclature for UCSC cytoband tracks
ucsc
ucsctrack
ggbio
Gviz
hg19
updated 7.8 years ago by
maximilianh
▴ 10 • written 7.8 years ago by
metamaden
▴ 10
0
votes
0
replies
1.4k
views
Error IdeoViz package: getIdeo
IdeoViz
UCSC
download_error
7.8 years ago
kaleb.gatto
• 0
0
votes
5
replies
3.1k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer
mm9
ucsc
updated 8.4 years ago by
Martin Morgan
25k • written 9.6 years ago by
krijgerp
• 0
2
votes
32
replies
5.5k
views
Gviz error 'Expectation Failed'
gviz
ucsc
8.5 years ago • updated 8.4 years ago
Tom
▴ 10
2
votes
3
replies
2.6k
views
Loading BSgenome.Hsapiens.UCSC.hg19 package
ucsc
bsgenome.hsapiens.ucsc.hg19
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
Sushant Pawar
• 0
0
votes
1
reply
1.5k
views
Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
gviz
ucsc
updated 8.7 years ago by
Robert Ivanek
▴ 750 • written 8.7 years ago by
just
• 0
3
votes
5
replies
1.9k
views
UcscTrack and BED without headers
gviz
BED
Ucsc
UcscTrack
8.9 years ago
Andy91
▴ 60
1
vote
4
replies
2.8k
views
It is possible to use Gviz without a valid UCSC genome?
gviz
UCSC
updated 9.0 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.0 years ago by
Vinicius Henrique da Silva
▴ 40
1
vote
2
replies
3.7k
views
Converting annotation from UCSC to Ensembl
ensembl
ucsc
annotation
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
AB
▴ 110
2
votes
2
replies
3.0k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.0 years ago by
Robert Castelo
★ 3.4k • written 9.0 years ago by
efoss
▴ 10
2
votes
10
replies
2.9k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer
ucsc
9.5 years ago
andrew.j.skelton73
▴ 370
0
votes
1
reply
1.8k
views
Using European UCSC server in Gviz
Gviz
UCSC
updated 9.5 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.6 years ago by
krijgerp
• 0
2
votes
2
replies
1.8k
views
UCSC Genome, match accession (NM_#####) with actual gene name
ucsc
gene set analysis
genome annotation
updated 9.6 years ago by
James W. MacDonald
67k • written 9.6 years ago by
n_bormann1
• 0
0
votes
2
replies
1.7k
views
Show the name of genetic elements and change the color according to its feature using UcscTrack
gviz
ucsc
9.8 years ago • updated 9.7 years ago
Tiphaine Martin
▴ 40
0
votes
1
reply
1.4k
views
Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures
genomicranges
ucsc
updated 9.9 years ago by
Hervé Pagès
16k • written 9.9 years ago by
Jake
▴ 90
29 results • Page
1 of 1
Recent ...
Replies
Answer: Epic v2 Annotation CpG_maf source?
by
James W. MacDonald
67k
Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…
Comment: Deseq2 res Function
by
James W. MacDonald
67k
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…
Answer: Struggle with the replicates of epic array data
by
James W. MacDonald
67k
You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Robert Castelo
★ 3.4k
So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Votes
Appropriate use of the function treat of the limma package
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
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