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Heatmap
•
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6
votes
25
replies
4.1k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps
heatmap
limma
updated 9.0 years ago by
cstrato
★ 3.9k • written 9.0 years ago by
Biologist
▴ 120
5
votes
11
replies
3.8k
views
Heatmap only including DE genes?
heatmap
coolmap
pheatmap
updated 4.9 years ago by
Gordon Smyth
52k • written 4.9 years ago by
Raito92
▴ 60
2
votes
10
replies
21k
views
Heatmap with error message: `x' must be a numeric matrix
r
heatmap
numericmatrix
updated 9.0 years ago by
Assa Yeroslaviz
★ 1.5k • written 9.0 years ago by
Biologist
▴ 120
9
votes
10
replies
14k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma
removeBatchEffect
heatmap
clustering
updated 9.2 years ago by
Bernd Klaus
▴ 610 • written 9.2 years ago by
Ekarl2
▴ 80
8
votes
8
replies
13k
views
Heatmap from DESeq2 DE genes
deseq2
heatmap
updated 10.2 years ago by
James W. MacDonald
68k • written 10.2 years ago by
Catalina Aguilar Hurtado
▴ 90
2
votes
8
replies
4.0k
views
removing batch effect using DESeq and sva
sva
deseq2
batch effect
PCA
heatmap
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
bioyas
▴ 10
0
votes
8
replies
1.9k
views
Regarding general understanding of DiffBind
diffbind
heatmap
8.8 years ago • updated 8.7 years ago
shubhibartaria
▴ 10
3
votes
7
replies
3.9k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix
heatmap
ComplexHeatmap
missing values
R
updated 5.5 years ago by
Zuguang Gu
▴ 290 • written 5.5 years ago by
mohammedtoufiq91
▴ 10
2
votes
7
replies
5.7k
views
Heatmap of a subset of genes
heatmap
written 8.9 years ago by
giroudpaul
▴ 40
4
votes
6
replies
20k
views
R studio input style for generating heatmap (RNAseq)
heatmap
r studio
log2foldchange
updated 5.1 years ago by
Steve Lianoglou
★ 13k • written 5.1 years ago by
alirezabcsaeidi
• 0
7
votes
6
replies
6.8k
views
scaling data for clustering heat map
edger
heatmap
clustering
differential gene expression
rnaseq
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
Beginner
▴ 60
0
votes
6
replies
2.2k
views
Breaking down the output from plotEigengeneNetworks()
WGCNA
Heatmap
EigenGeneNetworks
5.4 years ago
l.s.wijaya
• 0
2
votes
5
replies
5.8k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna
heatmap
desq2
clustering
updated 9.9 years ago by
Dario Strbenac
★ 1.6k • written 9.9 years ago by
Jon Bråte
▴ 260
0
votes
5
replies
2.1k
views
What color is assigned in heatmap for time series analysis
deseq2
time course
heatmap
updated 8.8 years ago by
EagleEye
▴ 10 • written 8.8 years ago by
rahel14350
▴ 10
3
votes
5
replies
2.5k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma
heatmap
DEGs
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
lawarde.ankita1
▴ 30
1
vote
5
replies
5.2k
views
Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
heatmap.2
heatmap
edgeR
deseq2
deseq
updated 8.9 years ago by
Michael Love
43k • written 8.9 years ago by
Zain A Alvi
▴ 10
1
vote
4
replies
1.6k
views
Methylation profile through chromosome
R
heatmap
8.6 years ago
Adam
• 0
4
votes
4
replies
10k
views
ComplexHeatmap Scale by Row
ComplexHeatmap
heatmap
updated 9.8 years ago by
James W. MacDonald
68k • written 9.8 years ago by
andrew.j.skelton73
▴ 370
1
vote
4
replies
2.2k
views
Is there a way to align Hi-C half heatmaps to Gviz track?
Gviz
Hi-C
Heatmap
updated 8.9 years ago by
Nicolas Servant
▴ 260 • written 8.9 years ago by
Merienne Nicolas
▴ 120
0
votes
4
replies
1.7k
views
PureCN optimum solution vs heat map
PureCN
Solution
Heatmap
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
0
votes
4
replies
2.6k
views
HUgene 2.0 analyses heatmap
hugene20
heatmap
affymetrixchip
updated 9.8 years ago by
alakatos
▴ 130 • written 9.9 years ago by
kanacska
▴ 10
2
votes
3
replies
4.7k
views
Deseq2. Cluster of an specific list
deseq2
heatmap
clustering
file
list
updated 9.5 years ago by
Michael Love
43k • written 9.5 years ago by
chariko
• 0
0
votes
3
replies
991
views
how to draw multiple heatmap from GeneOverlap
GeneOverlap
multiple figures
heatmap
updated 5.1 years ago by
James W. MacDonald
68k • written 5.1 years ago by
C T
▴ 140
2
votes
3
replies
1.9k
views
RNAseq and heatmap
deseq2
RNA-seq
Heatmap
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
Merlin
▴ 10
1
vote
3
replies
2.0k
views
DESeq2 with paired data Heatmap
deseq2
heatmap
updated 8.8 years ago by
Steve Lianoglou
★ 13k • written 8.8 years ago by
l.weissenburgermoser
• 0
1
vote
3
replies
1.7k
views
Interpretation of LRT results
DESeq2
LRT
Heatmap
updated 17 months ago by
James W. MacDonald
68k • written 2.4 years ago by
Laia
▴ 10
6
votes
3
replies
7.2k
views
Heatmap Plotting in R
heatmap
R
bioconductor
9.7 years ago • updated 8.0 years ago
Deepak Tanwar
▴ 10
0
votes
2
replies
6.2k
views
Plots and Heat Maps not displaying in RGui Window
plot
heatmap
graphical
rnaseqgene
deseqdataset
9.9 years ago
greg.mulhearn
• 0
0
votes
2
replies
1.7k
views
a newbie question on ConsensusClusterPlus
consensusclusterplus
heatmap
5.6 years ago
niki.nowhere
• 0
3
votes
2
replies
2.8k
views
Complex Heatmap shows just one color
Heatmap
ComplexHeatmap
colorRamp
3.9 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
4.9k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 5.6 years ago by
mikhael.manurung
▴ 280 • written 5.6 years ago by
danikadigiacomo
• 0
1
vote
2
replies
1.6k
views
Obtain the first gene expression heatmaps from GOexpress package gene ontology enrichment analysis results
GOexpress
heatmap
gene ontology
plot
updated 5.4 years ago by
kevin.rue
▴ 350 • written 5.4 years ago by
Antonio Campos
• 0
1
vote
2
replies
2.3k
views
Diffbind: how to include all the samples in the heatmap while using the contrast
diffbind
heatmap
correlation
updated 8.0 years ago by
Rory Stark
★ 5.2k • written 8.0 years ago by
a.bahraini88
• 0
0
votes
2
replies
5.7k
views
DESeq2: how to interpret the heatmap clustering samples
deseq2
rlog transformation
heatmap
scale
8.0 years ago
lina.faller
▴ 10
1
vote
2
replies
1.3k
views
genes repeated in the heatmap several times(10x) when using limma
limma
normalization
heatmap
design and contrast matrix
cancer
updated 6.4 years ago by
Axel Klenk
★ 1.1k • written 6.4 years ago by
andreilazar9
• 0
0
votes
2
replies
1.5k
views
Error in heatmap()
heatmap
updated 9.2 years ago by
James W. MacDonald
68k • written 9.2 years ago by
libya.tahani
• 0
2
votes
2
replies
1.4k
views
Problem with using `GRheatmapData` function in compEpiTools package
compEpiTools
error
heatmap
updated 7.5 years ago by
mattia pelizzola
▴ 200 • written 7.5 years ago by
ma1478
• 0
0
votes
2
replies
1.4k
views
expression pattern tracking of some defined gene in a microarray by heatmap
heatmap
microarray
9.7 years ago
Angel
▴ 40
1
vote
2
replies
2.7k
views
Supervised clustering by sample
hclust
heatmap
10.1 years ago
rmgreer
• 0
1
vote
2
replies
1.2k
views
What are the expression value of genes/probes in limma results of topTable
Heatmap
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
rkp
• 0
5
votes
2
replies
16k
views
Complex Heatmap - hide one legend, show 2 - out off three annotations
complexheatmap
bioconductor
annotation
heatmap
legend
8.9 years ago • updated 8.8 years ago
annkatrin.goepfert
▴ 10
0
votes
1
reply
2.0k
views
Error when trying to create a heatmap with DESeq2
Heatmap
RNA-seqanalysis
heatmaps
DESeq2
updated 16 months ago by
Basti
▴ 780 • written 16 months ago by
langziv
• 0
0
votes
1
reply
1.5k
views
Larger values masking others for OmicCircos heatmap
differential gene expression
heatmap
Circos
omiccircos
10.2 years ago
Peter.Wood
• 0
0
votes
1
reply
7.7k
views
plotting heatmap from DESeqDataSet
deseq2
heatmap
updated 9.6 years ago by
Michael Love
43k • written 9.6 years ago by
nishikant.wase
• 0
0
votes
1
reply
2.7k
views
Display subset of rownames in large heatmap?
heatmap
rownames
genes
9.5 years ago
johnlee.johnson
• 0
1
vote
1
reply
1.5k
views
reactive CellCODE heatmap
cellcode
shiny
heatmap
updated 8.9 years ago by
Andrzej Oleś
▴ 750 • written 8.9 years ago by
christopher.clarskon15
▴ 20
2
votes
1
reply
1.9k
views
DiffBind affinity vs occupancy Heatmaps
diffbind
heatmap
pearsoncorrelation
updated 8.7 years ago by
Rory Stark
★ 5.2k • written 8.7 years ago by
shubhibartaria
▴ 10
2
votes
1
reply
4.1k
views
Assign custom dendrogram to ComplexHeatmap Heatmap object
complexheatmap
heatmap.2
dendrogram
dendextend
heatmap
updated 8.4 years ago by
jokergoo
▴ 200 • written 8.4 years ago by
enricoferrero
▴ 680
0
votes
1
reply
1.5k
views
Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq
heatmap
updated 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
Key
• 0
0
votes
1
reply
2.3k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2
tpm
heatmap
pheatmap
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
50 results • Page
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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
clusterProfiler-GO enrichment Error
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
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