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ggplot2
•
reset
0
votes
7
replies
1.5k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
BioES
• 0
1
vote
5
replies
603
views
Mixed up sample info with plotPCA
plotMA
ggplot2
plotPCA
DESeq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
sara.jacobson
• 0
5
votes
11
replies
2.9k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 10 months ago by
Sabiha
▴ 20
0
votes
1
reply
546
views
How to add pvalue to boxplot?
boxplot
ggplot2
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
Sooni
▴ 10
0
votes
0
replies
932
views
GOplots::GOChord with heatmaps?
GOChord
ggplot2::geom_polygon()
GOplot
ggplot2
14 months ago
adrija.kalvisa
• 0
0
votes
2
replies
850
views
ggplot2 bar plot
R
Visualization
ggplot2
18 months ago
Jitendra
▴ 10
4
votes
6
replies
1.4k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
23 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.4k
views
Adjust color of ellipse in PCA plot from DESeq2 data set
stat_ellipse
DESeq2
ggplot2
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
thu.vo
• 0
0
votes
3
replies
2.5k
views
ggplot labels with linebreaks inn ggvenn venn diagram
ggvenn
ggplot2
3.6 years ago
anders.tondell
▴ 30
0
votes
4
replies
3.8k
views
ggplot2 of PCA
software error
ggplot2
updated 3.8 years ago by
leahfa
• 0 • written 3.8 years ago by
yueli7
▴ 20
0
votes
2
replies
1.8k
views
How to adjust and align timepoints on x-axis in the ggplot2
ggplot2
line plot
x-axis
data frame
R
4.4 years ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
690
views
Adding layer to legend in waterfall plot
GenVisR
ggplot2
waterfall
4.5 years ago
sheneicechang
• 0
0
votes
0
replies
685
views
Unable to obtain the line chart with error envelop in ggplot2 and geom_ribbon()
ggplot2
line chart
R
geom_ribbon()
4.5 years ago
mohammedtoufiq91
▴ 10
12
votes
7
replies
4.4k
views
Plot ggplot2 and ggbio Images Together
ggplot2
ggbio
cowplot
updated 4.7 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.9 years ago by
andrew.j.skelton73
▴ 370
0
votes
0
replies
647
views
How to plot "chromosomewise" "allele frequency" of a "Hybrid" in comparison to its "Inbred parents"
ggplot2
ggplot
cmplot
5.0 years ago
gens8094
• 0
0
votes
0
replies
635
views
How to plot "chromosomewise" "allele frequency" of a "Hybrid" in comparison to its "Inbred parents"
ggplot
cmplot
ggplot2
5.1 years ago
gens8094
• 0
2
votes
5
replies
3.7k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran
scater
Rtsne
ggplot2
scRNA-Seq
updated 20 months ago by
jamie.gearing
▴ 60 • written 5.2 years ago by
hamza_karakurt
▴ 50
0
votes
0
replies
1.2k
views
vcf to venn diagram
snps
vcf
venn diagram
ggplot2
5.3 years ago
mictadlo
▴ 10
0
votes
1
reply
857
views
plot get overridden rather to overlapped
rsamtools
ggplot2
plot
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
mictadlo
▴ 10
1
vote
2
replies
1.5k
views
ggbio won't plot ideogram in R version 3.3.1, ggplot2 version 3.1.0
ggbio
ggplot2
5.4 years ago
t.fadason
▴ 10
2
votes
2
replies
954
views
aes label in ggbio_1.26.1 with ggplot2_3.0.0
ggbio
ggplot2
5.6 years ago
Lescai, Francesco
▴ 380
0
votes
1
reply
1.0k
views
display of chromosomes (on the linear scale) and translocations
ggviz
ggplot2
gviz
circlize
Rcircos
5.7 years ago
Bogdan
▴ 670
0
votes
0
replies
1.8k
views
ggbio Error: Don't know how to add o to a plot
software error
ggbio
ggplot2
5.8 years ago
zhe
▴ 20
0
votes
2
replies
3.0k
views
Add annotation color bar to ggplot
ggplot2
annotation
updated 6.0 years ago by
TriS
▴ 200 • written 6.0 years ago by
da.de
▴ 30
5
votes
12
replies
10k
views
Combining ComplexHeatmap with other plot types
complexheatmap
ggplot2
updated 6.4 years ago by
Zuguang Gu
▴ 260 • written 6.4 years ago by
my4
▴ 10
3
votes
4
replies
3.4k
views
saving a plot as png and also showing inside Rstudio
edger
ggplot2
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
mictadlo
▴ 10
6
votes
2
replies
6.3k
views
How is it possible to get a legend outside plotMDS?
edger
ggplot2
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
mictadlo
▴ 10
0
votes
1
reply
1.0k
views
Pseudo-coloring DiffBind volcano plot
diffbind
chipseq
volcanoplot
ggplot2
updated 6.5 years ago by
Rory Stark
★ 5.1k • written 6.5 years ago by
rbronste
▴ 60
2
votes
3
replies
2.1k
views
MA plot DiffBind in ggplot2
diffbind
ggplot2
r
chipseq
updated 6.6 years ago by
Rory Stark
★ 5.1k • written 6.6 years ago by
reubenmcgregor88
• 0
2
votes
0
replies
1.9k
views
Gviz plot combined with multiple ggplot2 plots
gviz
gviz-package
ggplot2
6.6 years ago
christian.aichmueller
▴ 20
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.7 years ago
lauren.czaplicki
• 0
0
votes
2
replies
1.4k
views
ggplots gives errors
rnaseq
ggplot2
updated 6.7 years ago by
Matthias Z.
▴ 20 • written 6.7 years ago by
ucheuna
• 0
5
votes
3
replies
1.5k
views
Using BiocStyle with plotly
biocstyle
plotly
ggplot2
updated 6.8 years ago by
Andrzej Oleś
▴ 750 • written 6.8 years ago by
Lluís Revilla Sancho
▴ 730
2
votes
2
replies
4.2k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2
clusterprofiler
visualization
gseGo
7.0 years ago • updated 3.4 years ago
tcalvo
▴ 90
0
votes
1
reply
3.3k
views
an error in ggbio: "Breaks and labels are different lengths"
ggbio
ggplot2
7.0 years ago
Bogdan
▴ 670
0
votes
1
reply
2.0k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
matthew.wipperman
• 0
0
votes
2
replies
1.8k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 7.1 years ago by
Michael Love
41k • written 7.1 years ago by
sarahmacdonald86
• 0
0
votes
1
reply
1.3k
views
Metagene: file import and aesthetic customization
metagene
R
ggplot2
updated 7.2 years ago by
Charles Joly Beauparlant
▴ 170 • written 7.2 years ago by
JunLVI
▴ 40
1
vote
3
replies
2.8k
views
Combining LD matrix plot with SNP and gene data with ggplot / ggbio tracks() function
ggplot2
ggbio
plot
tracks
bioconductor
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
oswaldo.lorenzo
▴ 10
0
votes
5
replies
1.4k
views
How to plot benchmark result of R/ Bioconductor package (getting curve or line graph)?
r
benchmark
performance
ggplot2
7.3 years ago
Jurat Shahidin
▴ 80
2
votes
4
replies
1.3k
views
ggbio tracks () does not allow "call" class in the "main" slot of the function
ggbio
ggplot2
call
plot
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
oswaldo.lorenzo
▴ 10
0
votes
2
replies
1.4k
views
tracks () function from ggbio does not allow italic expression in the title
ggbio
ggplot2
title
typography
7.6 years ago • updated 7.3 years ago
oswaldo.lorenzo
▴ 10
0
votes
0
replies
1.6k
views
Select what conditionsto graph in Report tools with Deseq containing multiple conditions
deseq2
ggplot2
reportingtools
7.4 years ago
abass.conteh
• 0
0
votes
1
reply
948
views
Building a pseudo-network based on correlations
R
ggplot2
updated 7.5 years ago by
Matthias Z.
▴ 20 • written 7.5 years ago by
ssabri
▴ 20
0
votes
1
reply
2.0k
views
Missing levels in legend using autoplot () + scale_color_manual () functions
ggbio
ggplot2
legend
bioconductor
karyiogram
7.6 years ago
oswaldo.lorenzo
▴ 10
1
vote
1
reply
1.6k
views
How to show chromosome position and SNP label at the same time in x axis
ggbio
ggplot2
genomics
plot
7.6 years ago
oswaldo.lorenzo
▴ 10
0
votes
1
reply
2.3k
views
Ideogram not alligned with ggbio and tracks()
ggbio
ggplot2
updated 7.6 years ago by
oswaldo.lorenzo
▴ 10 • written 8.0 years ago by
my4
▴ 10
2
votes
3
replies
1.7k
views
ggbio tracks() function handling x axis in the wrong way
ggbio
ggplot2
tracks
genomics
plot
7.6 years ago
oswaldo.lorenzo
▴ 10
2
votes
2
replies
1.3k
views
Anyone know how to make a plot like this - I don't even know what it's called.
plot
ggplot2
updated 7.8 years ago by
WouterDeCoster
▴ 130 • written 7.8 years ago by
clairelsimpson
▴ 10
0
votes
2
replies
1.8k
views
displaying UP, DOWN, and NON-regulated genes
ggplot2
8.2 years ago
Bogdan
▴ 670
50 results • Page
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Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize
by
James W. MacDonald
65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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