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UCSC
•
reset
3
votes
5
replies
1.7k
views
UcscTrack and BED without headers
gviz
BED
Ucsc
UcscTrack
8.3 years ago
Andy91
▴ 60
2
votes
32
replies
4.8k
views
Gviz error 'Expectation Failed'
gviz
ucsc
7.9 years ago • updated 7.8 years ago
Tom
▴ 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
max
▴ 10 • written 6.0 years ago by
chrisamiller
• 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
maximilianh
▴ 10 • written 9.1 years ago by
James Perkins
▴ 60
0
votes
6
replies
1.4k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq
methylation
ensembl
ucsc
limma
6.2 years ago • updated 6.1 years ago
dusan.petrovic
• 0
3
votes
4
replies
1.4k
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 6.8 years ago by
Valerie Obenchain
★ 6.8k • written 6.9 years ago by
Lna
• 0
0
votes
2
replies
1.6k
views
Show the name of genetic elements and change the color according to its feature using UcscTrack
gviz
ucsc
9.2 years ago • updated 9.1 years ago
Tiphaine Martin
▴ 40
1
vote
4
replies
2.6k
views
It is possible to use Gviz without a valid UCSC genome?
gviz
UCSC
updated 8.4 years ago by
florian.hahne@novartis.com
★ 1.6k • written 8.4 years ago by
Vinicius Henrique da Silva
▴ 40
1
vote
4
replies
1.0k
views
Simple UCSC to transcript annotation
annotation
ucsc
tdx
transcripts
6.8 years ago
AntonS
• 0
2
votes
3
replies
2.4k
views
Loading BSgenome.Hsapiens.UCSC.hg19 package
ucsc
bsgenome.hsapiens.ucsc.hg19
updated 8.1 years ago by
Martin Morgan
25k • written 8.1 years ago by
Sushant Pawar
• 0
1
vote
4
replies
2.6k
views
Giemsa stain annotation/nomenclature for UCSC cytoband tracks
ucsc
ucsctrack
ggbio
Gviz
hg19
updated 7.2 years ago by
maximilianh
▴ 10 • written 7.2 years ago by
metamaden
▴ 10
0
votes
2
replies
1.4k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 6.8 years ago by
Valerie Obenchain
★ 6.8k • written 6.8 years ago by
Lna
• 0
0
votes
1
reply
1.1k
views
Gviz error in IdeogramTrack command
Gviz
ucsc
6.5 years ago
Taiki Tsutsui
▴ 10
0
votes
1
reply
1.3k
views
Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures
genomicranges
ucsc
updated 9.3 years ago by
Hervé Pagès
16k • written 9.3 years ago by
Jake
▴ 90
2
votes
4
replies
1.4k
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 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
olavur
▴ 10
2
votes
3
replies
1.7k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
foehn
▴ 100
1
vote
1
reply
2.6k
views
TxDb.Hsapiens.UCSC.hg38.knownGene In install.packages(pkgs = doing, lib = lib, ...) Non-Zero Exit Status
annotation
UCSC
doing
lib
mgcv
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
tdfyoder
• 0
3
votes
4
replies
1.1k
views
Convert a bed file to bigBed with rtracklayer
bed
bigBed
rtracklayer
ucsc
17 months ago
L
▴ 50
2
votes
10
replies
2.6k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer
ucsc
8.9 years ago
andrew.j.skelton73
▴ 370
2
votes
2
replies
1.6k
views
UCSC Genome, match accession (NM_#####) with actual gene name
ucsc
gene set analysis
genome annotation
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
n_bormann1
• 0
0
votes
5
replies
2.8k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer
mm9
ucsc
updated 7.8 years ago by
Martin Morgan
25k • written 9.0 years ago by
krijgerp
• 0
0
votes
1
reply
1.6k
views
Using European UCSC server in Gviz
Gviz
UCSC
updated 8.9 years ago by
florian.hahne@novartis.com
★ 1.6k • written 9.0 years ago by
krijgerp
• 0
2
votes
2
replies
2.6k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 8.4 years ago by
Robert Castelo
★ 3.3k • written 8.4 years ago by
efoss
▴ 10
1
vote
2
replies
3.4k
views
Converting annotation from UCSC to Ensembl
ensembl
ucsc
annotation
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
AB
▴ 110
0
votes
1
reply
1.3k
views
Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
gviz
ucsc
updated 8.2 years ago by
Robert Ivanek
▴ 730 • written 8.2 years ago by
just
• 0
1
vote
0
replies
430
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
5 months ago
yujin
▴ 10
0
votes
0
replies
1.2k
views
Error IdeoViz package: getIdeo
IdeoViz
UCSC
download_error
7.2 years ago
kaleb.gatto
• 0
0
votes
2
replies
1.2k
views
How to get UCSC url when use rtracklayer, contain the track in the url ,it may be very useful
rtracklayer
UCSC
ucsctrack
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
zhangqshxxzz
• 0
28 results • Page
1 of 1
Recent ...
Replies
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…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
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)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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