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Gviz
•
reset
0
votes
0
replies
44
views
Simple confidence intervall Gviz
Gviz
11 days ago
William
• 0
0
votes
1
reply
1.4k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate
Gviz
updated 11 weeks ago by
ming
• 0 • written 3.3 years ago by
Ahdee
▴ 50
0
votes
0
replies
241
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage
Gviz
sashimi
5 months ago
Marco
• 0
0
votes
3
replies
1.6k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz
Saccharomyces_cerevisiae
Gviz
ideogram
updated 7 months ago by
Maryna
• 0 • written 18 months ago by
Michael
• 0
0
votes
3
replies
585
views
Gviz and custom database
Gviz
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
luigi.faino
• 0
1
vote
2
replies
1.9k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 11 months ago by
Tim Peters
▴ 230 • written 2.1 years ago by
jose.ramirez1
▴ 10
0
votes
1
reply
502
views
GC content track on GVIZ
Gviz
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
ilaria.maurizio
• 0
1
vote
3
replies
2.2k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 16 months ago by
Robert Ivanek
▴ 750 • written 3.9 years ago by
ltzhou
• 0
0
votes
0
replies
650
views
Gviz::GeneRegionTrack error with standard TxDb: "adding seqlevels to a TxDb object is not supported"
Gviz
16 months ago
dbsgtk
• 0
1
vote
0
replies
841
views
Gviz : UcscTrack
rtracklayer
UCSC
Gviz
16 months ago
yujin
▴ 10
1
vote
3
replies
941
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer
Gviz
updated 16 months ago by
Hervé Pagès
16k • written 16 months ago by
yujin
▴ 10
0
votes
5
replies
2.5k
views
Gviz: UcscTrack and "GC Percent" information
Gviz
coMET
2.3 years ago • updated 17 months ago
Daniel E. Weeks
▴ 30
0
votes
2
replies
804
views
how to add annotation on individual track
Gviz
updated 22 months ago by
Robert Ivanek
▴ 750 • written 22 months ago by
xiaofeiwang18266
▴ 50
0
votes
0
replies
619
views
Coloring reads in AlignmentsTrack based on mapq
Gviz
2.1 years ago
Vinicius Henrique da Silva
▴ 40
0
votes
0
replies
981
views
DMR.plot "Error: Too many stacks to draw"
DMRcate
Gviz
GV
2.1 years ago
gilliangoobie
• 0
0
votes
2
replies
1.7k
views
Gviz: Filtering AlignmentsTrack by read names
Gvi
Gviz
updated 2.6 years ago by
James W. MacDonald
68k • written 2.7 years ago by
anikajohn
• 0
0
votes
1
reply
1.4k
views
GViz plot coverage for multiple chromosome and multiple samples using BAM files and save them as a single pdf report
Gviz
2.7 years ago
rohitsatyam102
▴ 20
4
votes
1
reply
2.2k
views
How to add gene symbol in GeneRegionTrack in Gviz
Gviz
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
hsf378
• 0
1
vote
3
replies
2.5k
views
GVIZ giving error with loading hg38 genome
R
Gviz
2.9 years ago
RUser743
• 0
1
vote
2
replies
1.9k
views
Gviz and datatracks
Gviz
updated 3.1 years ago by
corinne_hutfilz
• 0 • written 3.2 years ago by
Bogdan
▴ 670
0
votes
0
replies
751
views
Color of 2nd exon
GViz
3.2 years ago
underscore
• 0
1
vote
1
reply
1.2k
views
Gviz DataTrack data transformation on the fly
aggregation
Gviz
DataTrack
updated 3.2 years ago by
Robert Ivanek
▴ 750 • written 3.2 years ago by
Robert
▴ 10
0
votes
0
replies
879
views
Modify y axis or add second y axis in Gviz
OverlayTrack
Gviz
3.2 years ago
Robert
▴ 10
4
votes
4
replies
2.8k
views
Gviz: ylim of the AlignmentsTrack
gviz
gviz-package
updated 3.2 years ago by
Pariksheet Nanda
▴ 120 • written 6.5 years ago by
wsciekly.maciek
▴ 10
0
votes
0
replies
770
views
Y axis Data Track GVIZ
GVIZ
3.4 years ago • updated 3.3 years ago
rbenel
▴ 40
1
vote
1
reply
1.9k
views
GVIZ on R not loading mm10 from UCSC
Gviz
3.5 years ago
RUser743
• 0
0
votes
3
replies
1.2k
views
Details AnnotationTrack swap densityplot and connectors
Gviz
3.5 years ago
Hartorthereal
• 0
1
vote
3
replies
1.7k
views
Gradient dotplot
Gviz
3.5 years ago
sophieagger
• 0
0
votes
0
replies
1.1k
views
One read per line and other ordering of reads in Gviz
Gviz
3.5 years ago
pillailab1
• 0
0
votes
4
replies
1.6k
views
window parameter in DataTrack function with a single sample
Gviz
3.6 years ago • updated 3.4 years ago
rbenel
▴ 40
0
votes
1
reply
1.4k
views
Gviz: change position of transcriptAnnotation
Gviz
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
mar.pieraccioli
▴ 10
0
votes
4
replies
1.7k
views
AlignmentsTrack empty plot
Coverage
RNASeq
plot
Gviz
updated 2.2 years ago by
James W. MacDonald
68k • written 3.6 years ago by
karlaarz
• 0
1
vote
3
replies
1.5k
views
Can't produce a generegiontrack from my txdb anymore
gviz
GenomicFeatures
3.6 years ago
A.J.
▴ 20
0
votes
0
replies
1.1k
views
Combining dataTracks in Gviz by averaging or subtraction
Gviz
3.8 years ago
gdeniz
• 0
0
votes
0
replies
990
views
Gviz - Fixed width of title panel on left
Gviz
3.9 years ago
rheery
• 0
0
votes
0
replies
889
views
Gviz: set colors for UTRs
plot
color
Gviz
utr
4.0 years ago
ginlucks
• 0
0
votes
3
replies
1.3k
views
Gviz featureAnnotation disappear when zooming in
Gviz
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
svenbioinf
• 0
0
votes
0
replies
1.2k
views
Gviz import lor reads from bam file
Gviz
longreads
4.0 years ago
ginlucks
• 0
0
votes
1
reply
967
views
two tracks have the same axis
plot
Gviz
4.3 years ago
腾
• 0
0
votes
2
replies
1.3k
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation
Alignment
Gviz
4.4 years ago
Vaibhav
• 0
0
votes
2
replies
1.3k
views
Gviz vertical text labels
Gviz
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
Jake
▴ 90
0
votes
1
reply
1.2k
views
Gviz, keeping strand information while zooming in
Gviz
strand
4.5 years ago
svenbioinf
• 0
2
votes
2
replies
1.6k
views
Can't display protein domain data from UCSC table unipDomain using Gviz
Gviz
protein
visualization
UcscTrack
protein domains
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
paul.jaschke
▴ 10
0
votes
1
reply
1.2k
views
Gviz package for plotting DMRs
Gviz
DMRs
updated 4.7 years ago by
Robert Ivanek
▴ 750 • written 4.7 years ago by
ayeshatariq78
• 0
0
votes
3
replies
2.8k
views
Is it possible to group multiple bigWig files in Gviz DataTrack?
Gviz
4.7 years ago
roman.hillje
• 0
1
vote
3
replies
1.1k
views
Highlight uniq transcripts in Gviz
Gviz
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
peris_baba
• 0
0
votes
2
replies
1.3k
views
Gviz AlignmentsTrack: how to prevent reads from overlapping each other
Gviz
updated 4.9 years ago by
Robert Ivanek
▴ 750 • written 4.9 years ago by
ari.loytynoja
• 0
0
votes
2
replies
1.4k
views
Error in value[[3L]](cond) : 'end' must be <= 536870912 with Gviz::plotTracks
Gviz
plotTracks
updated 5.1 years ago by
Robert Ivanek
▴ 750 • written 5.1 years ago by
syliang
• 0
0
votes
4
replies
1.5k
views
col.interactions.types for gviz InteractionTrack from the GenomicInteractions
GenomicInteractions
gviz
updated 5.1 years ago by
liz.ingsimmons
▴ 140 • written 5.1 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
1.2k
views
How to modify centromere depiction in Gviz IdeogramTrack?
Gviz
updated 5.1 years ago by
Robert Ivanek
▴ 750 • written 5.7 years ago by
Robert
▴ 10
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
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43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
A: use tximport's countsFromAbundance when using DESeq2
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