Showing : heatmap • reset
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 ▴ 610 • written 8.3 years ago by ▴ 80
8
votes
8
replies
12k
views
Heatmap from DESeq2 DE genes
deseq2 heatmap
updated 9.3 years ago by 65k • written 9.3 years ago by ▴ 90
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 50k • written 5.9 years ago by ▴ 60
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 ★ 3.9k • written 8.1 years ago by ▴ 110
6
votes
3
replies
6.9k
views
Heatmap Plotting in R
heatmap R bioconductor
8.7 years ago • updated 7.1 years ago Deepak Tanwar ▴ 10
5
votes
11
replies
2.5k
views
Heatmap only including DE genes?
heatmap coolmap pheatmap
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
5
votes
2
replies
13k
views
Complex Heatmap - hide one legend, show 2 - out off three annotations
complexheatmap bioconductor annotation heatmap legend
7.9 years ago • updated 7.8 years ago annkatrin.goepfert ▴ 10
4
votes
1
reply
2.4k
views
benefits of pearson distance for hierarchical clustering
heatmap.3 heatmap
updated 5.4 years ago by 65k • written 5.4 years ago by ▴ 50
4
votes
4
replies
9.2k
views
ComplexHeatmap Scale by Row
ComplexHeatmap heatmap
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 370
4
votes
6
replies
18k
views
R studio input style for generating heatmap (RNAseq)
heatmap r studio log2foldchange
updated 4.1 years ago by ★ 13k • written 4.2 years ago by • 0
3
votes
7
replies
3.1k
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 ▴ 260 • written 4.6 years ago by ▴ 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 50k • written 6.2 years ago by ▴ 30
3
votes
2
replies
2.0k
views
Complex Heatmap shows just one color
Heatmap ComplexHeatmap colorRamp
3.0 years ago Assa Yeroslaviz ★ 1.5k
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 ★ 1.5k • written 8.1 years ago by ▴ 110
2
votes
2
replies
1.1k
views
Problem with using `GRheatmapData` function in compEpiTools package
compEpiTools error heatmap
updated 6.5 years ago by ▴ 200 • written 6.5 years ago by • 0
2
votes
7
replies
4.9k
views
Heatmap of a subset of genes
heatmap
written 8.0 years ago by ▴ 40
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 8.9 years ago by ★ 1.5k • written 8.9 years ago by ▴ 250
2
votes
8
replies
3.2k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 10
2
votes
3
replies
1.6k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 10
2
votes
1
reply
1.5k
views
DiffBind affinity vs occupancy Heatmaps
diffbind heatmap pearsoncorrelation
updated 7.8 years ago by ★ 5.1k • written 7.8 years ago by ▴ 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 ▴ 200 • written 7.5 years ago by ▴ 660
2
votes
3
replies
4.2k
views
Deseq2. Cluster of an specific list
deseq2 heatmap clustering file list
updated 8.6 years ago by 41k • written 8.6 years ago by • 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 ★ 5.1k • written 7.1 years ago by • 0
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 ★ 1.0k • written 5.5 years ago by • 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 ▴ 350 • written 4.5 years ago by • 0
1
vote
4
replies
1.3k
views
Methylation profile through chromosome
R heatmap
7.7 years ago Adam • 0
1
vote
2
replies
2.4k
views
Supervised clustering by sample
hclust heatmap
9.2 years ago rmgreer • 0
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 41k • written 8.0 years ago by ▴ 10
1
vote
1
reply
1.3k
views
reactive CellCODE heatmap
cellcode shiny heatmap
updated 8.0 years ago by ▴ 750 • written 8.0 years ago by ▴ 20
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 65k • written 5.2 years ago by • 0
1
vote
3
replies
1.6k
views
DESeq2 with paired data Heatmap
deseq2 heatmap
updated 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
1
vote
1
reply
1.1k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by • 0
1
vote
1
reply
951
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by • 0
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 ▴ 260 • written 8.0 years ago by ▴ 120
1
vote
2
replies
971
views
What are the expression value of genes/probes in limma results of topTable
Heatmap
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
620
views
Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 5 months ago by ▴ 770 • written 5 months ago by • 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
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
4
replies
2.3k
views
HUgene 2.0 analyses heatmap
hugene20 heatmap affymetrixchip
updated 8.9 years ago by ▴ 130 • written 8.9 years ago by ▴ 10
0
votes
0
replies
970
views
metagenomeSeq heatmap error
heatmap
8.9 years ago PJ • 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
0
votes
1
reply
7.2k
views
plotting heatmap from DESeqDataSet
deseq2 heatmap
updated 8.7 years ago by 41k • written 8.7 years ago by • 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
0
votes
2
replies
1.2k
views
Error in heatmap()
heatmap
updated 8.3 years ago by 65k • written 8.3 years ago by • 0
0
votes
5
replies
1.7k
views
What color is assigned in heatmap for time series analysis
deseq2 time course heatmap
updated 7.8 years ago by ▴ 10 • written 7.8 years ago by ▴ 10
0
votes
8
replies
1.4k
views
Regarding general understanding of DiffBind
diffbind heatmap
7.8 years ago shubhibartaria ▴ 10
0
votes
0
replies
6.4k
views
Pheatmap: how to use breaks for pheatmap
pheatmap heatmap
7.5 years ago jarod_v6@libero.it ▴ 40
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 65k • written 7.1 years ago by • 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 • updated 7.0 years ago lina.faller • 0
0
votes
0
replies
1.5k
views
cummeRbund heatmap for specific isoforms (not genes)
cummerbund heatmap isoforms transcript_id
7.1 years ago domenico.somma • 0
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Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
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Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
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It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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