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Showing :
ggplot2
•
reset
0
votes
2
replies
1.8k
views
displaying UP, DOWN, and NON-regulated genes
ggplot2
8.2 years ago
Bogdan
▴ 670
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
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
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
3
votes
4
replies
2.7k
views
Bioconductor vignette on Time course experiments only describes how to plot the the gene with the smallest p-value. How can I plot specific genes of …
timecourse
time course
rna-seq
deseq2
ggplot2
8.6 years ago
moldach
▴ 20
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
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
1
vote
1
reply
1.8k
views
ggplot2 functions not inheriting?
ggplot2
8.3 years ago
andrew.j.skelton73
▴ 370
0
votes
2
replies
1.6k
views
error when using seeFastqPlot
systempiper
seeFastqPlot
software error
ggplot2
geom_histogram
updated 8.2 years ago by
Thomas Girke
★ 1.7k • written 8.2 years ago by
setarosd
• 0
1
vote
1
reply
1.5k
views
ggplot same data, different plots
ggplot2
ggplot
plot
updated 8.2 years ago by
James W. MacDonald
65k • written 8.2 years ago by
alptaciroglu
▴ 50
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
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
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
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
2
votes
2
replies
3.1k
views
cummeRbund change point size in volcano plot
cummerbund
ggplot2
size
r
volcanoplot
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
ianmisner17
▴ 20
1
vote
2
replies
2.7k
views
gene expression visualization: lineplot with ggplot2
ggplot2
lineplot
visualization
updated 8.9 years ago by
Jeremy Ng
▴ 180 • written 8.9 years ago by
alakatos
▴ 130
0
votes
1
reply
1.5k
views
Newbie - Adding Labels to Individual Genes with ggbio?
r
ggbio
ggplot2
dnaseq
genomicranges
updated 8.8 years ago by
arfranco
▴ 130 • written 8.8 years ago by
fathniz
• 0
0
votes
2
replies
2.9k
views
barplot with ggplot2 for gene expression
ggplot2
barplot
gene expression
gene expression
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
alakatos
▴ 130
0
votes
1
reply
1.4k
views
ggbio package only works with h19 genome
ggbio
ggplot2
updated 8.5 years ago by
James W. MacDonald
65k • written 8.5 years ago by
tiago211287
▴ 10
1
vote
4
replies
2.4k
views
Cannot get ggbio autoplot to run successfully on R 3.2 (3.2.2 or 3.2.3)
ggbio
ggplot2
autoplot
bioconductor
gene models
updated 8.2 years ago by
snf
▴ 10 • written 8.3 years ago by
danhovelson
▴ 10
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2
replies
847
views
ggplot2 bar plot
R
Visualization
ggplot2
18 months ago
Jitendra
▴ 10
1
vote
5
replies
600
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
544
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
1
reply
946
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
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
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
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
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
2
votes
2
replies
952
views
aes label in ggbio_1.26.1 with ggplot2_3.0.0
ggbio
ggplot2
5.6 years ago
Lescai, Francesco
▴ 380
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
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
0
replies
904
views
line colors plotRangesLinkedToData
ggbio
ggplot2
dexseq
8.3 years ago
Alejandro Reyes
★ 1.9k
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
0
replies
1.2k
views
vcf to venn diagram
snps
vcf
venn diagram
ggplot2
5.3 years ago
mictadlo
▴ 10
50 results • Page
1 of 1
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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