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6
votes
25
replies
3.2k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps
heatmap
limma
updated 8.1 years ago by
cstrato
★ 3.9k • written 8.1 years ago by
Biologist
▴ 110
5
votes
11
replies
2.5k
views
Heatmap only including DE genes?
heatmap
coolmap
pheatmap
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
Raito92
▴ 60
2
votes
10
replies
20k
views
Heatmap with error message: `x' must be a numeric matrix
r
heatmap
numericmatrix
updated 8.1 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.1 years ago by
Biologist
▴ 110
9
votes
10
replies
13k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 8.3 years ago by
Bernd Klaus
▴ 610 • written 8.3 years ago by
Ekarl2
▴ 80
8
votes
8
replies
12k
views
Heatmap from DESeq2 DE genes
deseq2
heatmap
updated 9.3 years ago by
James W. MacDonald
65k • written 9.3 years ago by
Catalina Aguilar Hurtado
▴ 90
2
votes
8
replies
3.3k
views
removing batch effect using DESeq and sva
sva
deseq2
batch effect
PCA
heatmap
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
bioyas
▴ 10
0
votes
8
replies
1.4k
views
Regarding general understanding of DiffBind
diffbind
heatmap
7.8 years ago
shubhibartaria
▴ 10
3
votes
7
replies
3.2k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix
heatmap
ComplexHeatmap
missing values
R
updated 4.6 years ago by
Zuguang Gu
▴ 260 • written 4.6 years ago by
mohammedtoufiq91
▴ 10
2
votes
7
replies
4.9k
views
Heatmap of a subset of genes
heatmap
written 8.0 years ago by
giroudpaul
▴ 40
4
votes
6
replies
18k
views
R studio input style for generating heatmap (RNAseq)
heatmap
r studio
log2foldchange
updated 4.2 years ago by
Steve Lianoglou
★ 13k • written 4.2 years ago by
alirezabcsaeidi
• 0
7
votes
6
replies
5.7k
views
scaling data for clustering heat map
edger
heatmap
clustering
differential gene expression
rnaseq
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Beginner
▴ 60
0
votes
6
replies
1.7k
views
Breaking down the output from plotEigengeneNetworks()
WGCNA
Heatmap
EigenGeneNetworks
4.5 years ago
l.s.wijaya
• 0
2
votes
5
replies
5.2k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna
heatmap
desq2
clustering
updated 9.0 years ago by
Dario Strbenac
★ 1.5k • written 9.0 years ago by
Jon Bråte
▴ 250
0
votes
5
replies
1.7k
views
What color is assigned in heatmap for time series analysis
deseq2
time course
heatmap
updated 7.9 years ago by
EagleEye
▴ 10 • written 7.9 years ago by
rahel14350
▴ 10
3
votes
5
replies
2.1k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma
heatmap
DEGs
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
lawarde.ankita1
▴ 30
1
vote
5
replies
4.2k
views
Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
heatmap.2
heatmap
edgeR
deseq2
deseq
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
Zain A Alvi
▴ 10
1
vote
4
replies
1.3k
views
Methylation profile through chromosome
R
heatmap
7.7 years ago
Adam
• 0
4
votes
4
replies
9.2k
views
ComplexHeatmap Scale by Row
ComplexHeatmap
heatmap
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
andrew.j.skelton73
▴ 370
1
vote
4
replies
1.8k
views
Is there a way to align Hi-C half heatmaps to Gviz track?
Gviz
Hi-C
Heatmap
updated 8.0 years ago by
Nicolas Servant
▴ 260 • written 8.0 years ago by
Merienne Nicolas
▴ 120
0
votes
4
replies
1.3k
views
PureCN optimum solution vs heat map
PureCN
Solution
Heatmap
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
0
votes
4
replies
2.3k
views
HUgene 2.0 analyses heatmap
hugene20
heatmap
affymetrixchip
updated 8.9 years ago by
alakatos
▴ 130 • written 9.0 years ago by
kanacska
▴ 10
2
votes
3
replies
4.3k
views
Deseq2. Cluster of an specific list
deseq2
heatmap
clustering
file
list
updated 8.6 years ago by
Michael Love
41k • written 8.6 years ago by
chariko
• 0
0
votes
3
replies
686
views
how to draw multiple heatmap from GeneOverlap
GeneOverlap
multiple figures
heatmap
updated 4.2 years ago by
James W. MacDonald
65k • written 4.2 years ago by
C T
▴ 140
2
votes
3
replies
1.6k
views
RNAseq and heatmap
deseq2
RNA-seq
Heatmap
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
Merlin
▴ 10
1
vote
3
replies
1.6k
views
DESeq2 with paired data Heatmap
deseq2
heatmap
updated 7.9 years ago by
Steve Lianoglou
★ 13k • written 7.9 years ago by
l.weissenburgermoser
• 0
0
votes
3
replies
918
views
Interpretation of LRT results
DESeq2
LRT
Heatmap
updated 6 months ago by
James W. MacDonald
65k • written 17 months ago by
Laia
▴ 10
6
votes
3
replies
6.9k
views
Heatmap Plotting in R
heatmap
R
bioconductor
8.8 years ago • updated 7.1 years ago
Deepak Tanwar
▴ 10
0
votes
2
replies
5.1k
views
Plots and Heat Maps not displaying in RGui Window
plot
heatmap
graphical
rnaseqgene
deseqdataset
9.0 years ago
greg.mulhearn
• 0
0
votes
2
replies
1.2k
views
a newbie question on ConsensusClusterPlus
consensusclusterplus
heatmap
4.7 years ago
niki.nowhere
• 0
3
votes
2
replies
2.0k
views
Complex Heatmap shows just one color
Heatmap
ComplexHeatmap
colorRamp
3.0 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
4.0k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 4.7 years ago by
mikhael.manurung
▴ 270 • written 4.7 years ago by
danikadigiacomo
• 0
1
vote
2
replies
1.2k
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress
heatmap
gene ontology
plot
updated 4.5 years ago by
kevin.rue
▴ 350 • written 4.5 years ago by
Antonio Campos
• 0
1
vote
2
replies
2.0k
views
Diffbind: how to include all the samples in the heatmap while using the contrast
diffbind
heatmap
correlation
updated 7.1 years ago by
Rory Stark
★ 5.2k • written 7.1 years ago by
a.bahraini88
• 0
0
votes
2
replies
4.8k
views
DESeq2: how to interpret the heatmap clustering samples
deseq2
rlog transformation
heatmap
scale
7.1 years ago
lina.faller
▴ 10
1
vote
2
replies
1.0k
views
genes repeated in the heatmap several times(10x) when using limma
limma
normalization
heatmap
design and contrast matrix
cancer
updated 5.5 years ago by
Axel Klenk
★ 1.0k • written 5.5 years ago by
andreilazar9
• 0
0
votes
2
replies
1.2k
views
Error in heatmap()
heatmap
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
libya.tahani
• 0
2
votes
2
replies
1.1k
views
Problem with using `GRheatmapData` function in compEpiTools package
compEpiTools
error
heatmap
updated 6.6 years ago by
mattia pelizzola
▴ 200 • written 6.6 years ago by
ma1478
• 0
0
votes
2
replies
1.2k
views
expression pattern tracking of some defined gene in a microarray by heatmap
heatmap
microarray
8.8 years ago
Angel
▴ 40
1
vote
2
replies
2.4k
views
Supervised clustering by sample
hclust
heatmap
9.2 years ago
rmgreer
• 0
1
vote
2
replies
978
views
What are the expression value of genes/probes in limma results of topTable
Heatmap
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
rkp
• 0
5
votes
2
replies
13k
views
Complex Heatmap - hide one legend, show 2 - out off three annotations
complexheatmap
bioconductor
annotation
heatmap
legend
8.0 years ago • updated 7.8 years ago
annkatrin.goepfert
▴ 10
0
votes
1
reply
648
views
Error when trying to create a heatmap with DESeq2
Heatmap
RNA-seqanalysis
heatmaps
DESeq2
updated 5 months ago by
Basti
▴ 780 • written 5 months ago by
langziv
• 0
0
votes
1
reply
1.3k
views
Larger values masking others for OmicCircos heatmap
differential gene expression
heatmap
Circos
omiccircos
9.3 years ago
Peter.Wood
• 0
0
votes
1
reply
7.2k
views
plotting heatmap from DESeqDataSet
deseq2
heatmap
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
nishikant.wase
• 0
0
votes
1
reply
2.4k
views
Display subset of rownames in large heatmap?
heatmap
rownames
genes
8.6 years ago
johnlee.johnson
• 0
1
vote
1
reply
1.3k
views
reactive CellCODE heatmap
cellcode
shiny
heatmap
updated 8.0 years ago by
Andrzej Oleś
▴ 750 • written 8.0 years ago by
christopher.clarskon15
▴ 20
2
votes
1
reply
1.5k
views
DiffBind affinity vs occupancy Heatmaps
diffbind
heatmap
pearsoncorrelation
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
shubhibartaria
▴ 10
2
votes
1
reply
3.5k
views
Assign custom dendrogram to ComplexHeatmap Heatmap object
complexheatmap
heatmap.2
dendrogram
dendextend
heatmap
updated 7.5 years ago by
jokergoo
▴ 200 • written 7.5 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.2k
views
Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq
heatmap
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
Key
• 0
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2
tpm
heatmap
pheatmap
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
jarod_v6@libero.it
▴ 40
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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'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
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
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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