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ucsc
•
reset
3
votes
4
replies
570
views
Convert a bed file to bigBed with rtracklayer
bed
bigBed
rtracklayer
ucsc
6 months ago
L
▴ 50
2
votes
3
replies
1.1k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 3.2 years ago by
James W. MacDonald
63k • written 3.2 years ago by
foehn
▴ 80
1
vote
1
reply
2.1k
views
TxDb.Hsapiens.UCSC.hg38.knownGene In install.packages(pkgs = doing, lib = lib, ...) Non-Zero Exit Status
annotation
UCSC
doing
lib
mgcv
updated 4.2 years ago by
James W. MacDonald
63k • written 4.2 years ago by
tdfyoder
• 0
2
votes
4
replies
983
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 4.5 years ago by
James W. MacDonald
63k • written 4.5 years ago by
olavur
▴ 10
3
votes
6
replies
1.4k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer
ucsc
ensgene
updated 5.1 years ago by
max
▴ 10 • written 5.1 years ago by
chrisamiller
• 0
0
votes
6
replies
1.1k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq
methylation
ensembl
ucsc
limma
5.3 years ago • updated 5.2 years ago
dusan.petrovic
• 0
0
votes
2
replies
881
views
How to get UCSC url when use rtracklayer, contain the track in the url ,it may be very useful
rtracklayer
UCSC
ucsctrack
updated 5.5 years ago by
James W. MacDonald
63k • written 5.5 years ago by
zhangqshxxzz
• 0
0
votes
1
reply
786
views
Gviz error in IdeogramTrack command
Gviz
ucsc
5.6 years ago
Taiki Tsutsui
▴ 10
1
vote
4
replies
775
views
Simple UCSC to transcript annotation
annotation
ucsc
tdx
transcripts
5.9 years ago
AntonS
• 0
0
votes
2
replies
986
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 5.9 years ago by
Valerie Obenchain
★ 6.8k • written 5.9 years ago by
Lna
• 0
3
votes
4
replies
1.1k
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 5.9 years ago by
Valerie Obenchain
★ 6.8k • written 6.0 years ago by
Lna
• 0
0
votes
3
replies
1.6k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer
browseGenome
save file
image
UCSC
updated 6.3 years ago by
maximilianh
▴ 10 • written 8.2 years ago by
James Perkins
▴ 60
1
vote
4
replies
2.0k
views
Giemsa stain annotation/nomenclature for UCSC cytoband tracks
ucsc
ucsctrack
ggbio
Gviz
hg19
updated 6.3 years ago by
maximilianh
▴ 10 • written 6.3 years ago by
metamaden
▴ 10
0
votes
0
replies
986
views
Error IdeoViz package: getIdeo
IdeoViz
UCSC
download_error
6.3 years ago
kaleb.gatto
• 0
0
votes
5
replies
2.5k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer
mm9
ucsc
updated 6.9 years ago by
Martin Morgan
25k • written 8.1 years ago by
krijgerp
• 0
2
votes
32
replies
3.6k
views
Gviz error 'Expectation Failed'
gviz
ucsc
7.0 years ago • updated 6.9 years ago
Tom
▴ 10
2
votes
3
replies
2.1k
views
Loading BSgenome.Hsapiens.UCSC.hg19 package
ucsc
bsgenome.hsapiens.ucsc.hg19
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Sushant Pawar
• 0
0
votes
1
reply
1.1k
views
Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
gviz
ucsc
updated 7.3 years ago by
Robert Ivanek
▴ 730 • written 7.3 years ago by
just
• 0
3
votes
5
replies
1.4k
views
UcscTrack and BED without headers
gviz
BED
Ucsc
UcscTrack
7.4 years ago
Andy91
▴ 60
1
vote
4
replies
2.2k
views
It is possible to use Gviz without a valid UCSC genome?
gviz
UCSC
updated 7.5 years ago by
florian.hahne@novartis.com
★ 1.6k • written 7.5 years ago by
Vinicius Henrique da Silva
▴ 40
1
vote
2
replies
3.1k
views
Converting annotation from UCSC to Ensembl
ensembl
ucsc
annotation
updated 7.5 years ago by
James W. MacDonald
63k • written 7.5 years ago by
AB
▴ 110
2
votes
2
replies
2.0k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 7.5 years ago by
Robert Castelo
★ 3.0k • written 7.5 years ago by
efoss
▴ 10
2
votes
10
replies
2.2k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer
ucsc
8.0 years ago
andrew.j.skelton73
▴ 360
0
votes
1
reply
1.4k
views
Using European UCSC server in Gviz
Gviz
UCSC
updated 8.0 years ago by
florian.hahne@novartis.com
★ 1.6k • written 8.1 years ago by
krijgerp
• 0
2
votes
2
replies
1.3k
views
UCSC Genome, match accession (NM_#####) with actual gene name
ucsc
gene set analysis
genome annotation
updated 8.1 years ago by
James W. MacDonald
63k • written 8.1 years ago by
n_bormann1
• 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
8.3 years ago • updated 8.2 years ago
Tiphaine Martin
▴ 40
0
votes
1
reply
1.1k
views
Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures
genomicranges
ucsc
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
Jake
▴ 90
27 results • Page
1 of 1
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Replies
Answer: DESeq2 + analysis question for design with uneven time point design
by
Michael Love
40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge
by
Michael Love
40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Gordon Smyth
47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting
by
ATpoint
★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Anna
▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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Gordon Smyth
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