Showing : Heatmap • reset
6
votes
25
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4.2k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps heatmap limma
updated 9.1 years ago by ★ 3.9k • written 9.1 years ago by ▴ 120
2
votes
10
replies
21k
views
Heatmap with error message: `x' must be a numeric matrix
r heatmap numericmatrix
updated 9.1 years ago by ★ 1.5k • written 9.1 years ago by ▴ 120
7
votes
6
replies
7.0k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 60
0
votes
5
replies
2.2k
views
What color is assigned in heatmap for time series analysis
deseq2 time course heatmap
updated 8.9 years ago by ▴ 10 • written 8.9 years ago by ▴ 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 6.5 years ago by ★ 1.1k • written 6.5 years ago by • 0
0
votes
8
replies
1.9k
views
Regarding general understanding of DiffBind
diffbind heatmap
8.9 years ago shubhibartaria ▴ 10
1
vote
2
replies
2.7k
views
Supervised clustering by sample
hclust heatmap
10.2 years ago rmgreer • 0
2
votes
7
replies
5.8k
views
Heatmap of a subset of genes
heatmap
written 9.0 years ago by ▴ 40
0
votes
2
replies
6.3k
views
Plots and Heat Maps not displaying in RGui Window
plot heatmap graphical rnaseqgene deseqdataset
10.0 years ago greg.mulhearn • 0
8
votes
8
replies
13k
views
Heatmap from DESeq2 DE genes
deseq2 heatmap
updated 10.3 years ago by 68k • written 10.3 years ago by ▴ 90
5
votes
11
replies
4.0k
views
Heatmap only including DE genes?
heatmap coolmap pheatmap
updated 5.0 years ago by 52k • written 5.0 years ago by ▴ 60
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 9.3 years ago by ▴ 610 • written 9.3 years ago by ▴ 80
6
votes
3
replies
7.3k
views
Heatmap Plotting in R
heatmap R bioconductor
9.8 years ago • updated 8.1 years ago Deepak Tanwar ▴ 10
1
vote
1
reply
1.6k
views
reactive CellCODE heatmap
cellcode shiny heatmap
updated 9.0 years ago by ▴ 750 • written 9.0 years ago by ▴ 20
1
vote
5
replies
5.3k
views
Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or DESeq2
heatmap.2 heatmap edgeR deseq2 deseq
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
5
votes
2
replies
17k
views
Complex Heatmap - hide one legend, show 2 - out off three annotations
complexheatmap bioconductor annotation heatmap legend
9.0 years ago • updated 8.9 years ago annkatrin.goepfert ▴ 10
1
vote
2
replies
1.2k
views
What are the expression value of genes/probes in limma results of topTable
Heatmap
updated 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
1
vote
3
replies
2.0k
views
DESeq2 with paired data Heatmap
deseq2 heatmap
updated 8.9 years ago by ★ 13k • written 8.9 years ago by • 0
2
votes
1
reply
2.0k
views
DiffBind affinity vs occupancy Heatmaps
diffbind heatmap pearsoncorrelation
updated 8.8 years ago by ★ 5.2k • written 8.8 years ago by ▴ 10
1
vote
4
replies
1.6k
views
Methylation profile through chromosome
R heatmap
8.7 years ago Adam • 0
2
votes
1
reply
4.2k
views
Assign custom dendrogram to ComplexHeatmap Heatmap object
complexheatmap heatmap.2 dendrogram dendextend heatmap
updated 8.5 years ago by ▴ 200 • written 8.5 years ago by ▴ 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 8.1 years ago by 68k • written 8.1 years ago by • 0
1
vote
2
replies
2.4k
views
Diffbind: how to include all the samples in the heatmap while using the contrast
diffbind heatmap correlation
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by • 0
0
votes
2
replies
5.8k
views
DESeq2: how to interpret the heatmap clustering samples
deseq2 rlog transformation heatmap scale
8.1 years ago lina.faller ▴ 10
2
votes
5
replies
5.9k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by ▴ 260
0
votes
4
replies
2.6k
views
HUgene 2.0 analyses heatmap
hugene20 heatmap affymetrixchip
updated 10.0 years ago by ▴ 130 • written 10.0 years ago by ▴ 10
0
votes
1
reply
2.3k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 40
0
votes
1
reply
1.8k
views
How to generate heatmap for three groups
rnaseq ruvseq heatmap
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
votes
1
reply
1.7k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.6 years ago by ★ 13k • written 7.7 years ago by • 0
2
votes
2
replies
1.4k
views
Problem with using `GRheatmapData` function in compEpiTools package
compEpiTools error heatmap
updated 7.6 years ago by ▴ 200 • written 7.6 years ago by • 0
0
votes
1
reply
1.7k
views
How to control the size of labels on heatmaps in DiffBind
diffbind labels heatmap
updated 7.4 years ago by ★ 5.2k • written 7.4 years ago by • 0
1
vote
1
reply
1.5k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
3
votes
5
replies
2.6k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma heatmap DEGs
updated 7.3 years ago by 52k • written 7.3 years ago by ▴ 30
1
vote
1
reply
1.2k
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 7.0 years ago by ★ 1.3k • written 7.0 years ago by • 0
0
votes
4
replies
1.8k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
0
votes
1
reply
1.3k
views
PureCN Solution Heatmap values
PureCN heatmap likelihoods
6.6 years ago twtoal ▴ 10
0
votes
1
reply
1.6k
views
SC3 how to customize plots ?
SC3 plot consensus marker heatmap
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by • 0
4
votes
1
reply
3.4k
views
benefits of pearson distance for hierarchical clustering
heatmap.3 heatmap
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 60
4
votes
4
replies
11k
views
ComplexHeatmap Scale by Row
ComplexHeatmap heatmap
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 370
1
vote
1
reply
1.8k
views
How to get the order of the gene list and indivdual cluster from the big heatmap made by heatmap2.0?
annotation heatmap
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
votes
2
replies
1.4k
views
expression pattern tracking of some defined gene in a microarray by heatmap
heatmap microarray
9.8 years ago Angel ▴ 40
2
votes
3
replies
1.9k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
2
votes
8
replies
4.1k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
votes
2
replies
5.0k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by • 0
3
votes
7
replies
4.1k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix heatmap ComplexHeatmap missing values R
updated 5.6 years ago by ▴ 290 • written 5.6 years ago by ▴ 10
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 5.6 years ago by ▴ 350 • written 5.6 years ago by • 0
0
votes
1
reply
7.8k
views
plotting heatmap from DESeqDataSet
deseq2 heatmap
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
3
replies
1.0k
views
how to draw multiple heatmap from GeneOverlap
GeneOverlap multiple figures heatmap
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 140
4
votes
6
replies
21k
views
R studio input style for generating heatmap (RNAseq)
heatmap r studio log2foldchange
updated 5.2 years ago by ★ 13k • written 5.2 years ago by • 0
2
votes
3
replies
4.7k
views
Deseq2. Cluster of an specific list
deseq2 heatmap clustering file list
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
Answer: How to formulate 2 factor nested design in DESeq2
A: Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
A: DESeq2 Dispersion Per Condition
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