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heatmap
•
reset
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
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
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
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
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
8
replies
1.4k
views
Regarding general understanding of DiffBind
diffbind
heatmap
7.8 years ago
shubhibartaria
▴ 10
1
vote
2
replies
2.4k
views
Supervised clustering by sample
hclust
heatmap
9.2 years ago
rmgreer
• 0
2
votes
7
replies
4.9k
views
Heatmap of a subset of genes
heatmap
written 8.0 years ago by
giroudpaul
▴ 40
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
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
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
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
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
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
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
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
1
vote
2
replies
976
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
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
2
votes
1
reply
1.5k
views
DiffBind affinity vs occupancy Heatmaps
diffbind
heatmap
pearsoncorrelation
updated 7.8 years ago by
Rory Stark
★ 5.1k • written 7.8 years ago by
shubhibartaria
▴ 10
1
vote
4
replies
1.3k
views
Methylation profile through chromosome
R
heatmap
7.7 years ago
Adam
• 0
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
1.1k
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
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
★ 5.1k • 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
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
4
replies
2.3k
views
HUgene 2.0 analyses heatmap
hugene20
heatmap
affymetrixchip
updated 8.9 years ago by
alakatos
▴ 130 • written 8.9 years ago by
kanacska
▴ 10
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
0
votes
1
reply
1.2k
views
How to generate heatmap for three groups
rnaseq
ruvseq
heatmap
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
manish20072013
• 0
0
votes
1
reply
1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 6.6 years ago by
Wolfgang Huber
★ 13k • written 6.6 years ago by
newmanss
• 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
1
reply
1.4k
views
How to control the size of labels on heatmaps in DiffBind
diffbind
labels
heatmap
updated 6.4 years ago by
Rory Stark
★ 5.1k • written 6.4 years ago by
epstein
• 0
1
vote
1
reply
1.1k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome
heatmap
metagenomeseq
updated 6.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.3 years ago by
arguello.rguez
• 0
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
1
reply
953
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap
chippeakanno
updated 6.0 years ago by
Ou, Jianhong
★ 1.3k • written 6.0 years ago by
gdeniz
• 0
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
1
reply
999
views
PureCN Solution Heatmap values
PureCN
heatmap
likelihoods
5.6 years ago
twtoal
▴ 10
0
votes
1
reply
1.3k
views
SC3 how to customize plots ?
SC3
plot
consensus
marker
heatmap
updated 5.4 years ago by
Vladimir Kiselev
▴ 150 • written 5.4 years ago by
shaktirielland
• 0
4
votes
1
reply
2.4k
views
benefits of pearson distance for hierarchical clustering
heatmap.3
heatmap
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
Ahdee
▴ 50
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
1
reply
1.3k
views
How to get the order of the gene list and indivdual cluster from the big heatmap made by heatmap2.0?
annotation
heatmap
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
shuvadeep.maity
• 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
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
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
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
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
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
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
3
replies
684
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
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
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
50 results • Page
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Comment: Different Shrunk Log2FC according with reference
by
Michael Love
41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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