Showing : heatmap • reset
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642
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Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
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0
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803
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
14 months ago gianni.drm • 0
0
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3
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916
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Interpretation of LRT results
DESeq2 LRT Heatmap
updated 6 months ago by 65k • written 17 months ago by ▴ 10
3
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2
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2.0k
views
Complex Heatmap shows just one color
Heatmap ComplexHeatmap colorRamp
3.0 years ago Assa Yeroslaviz ★ 1.5k
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0
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626
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How to overlap heatmaps on Gviz?
Givz heatmap overlap combine information
3.9 years ago kris.petrini • 0
5
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11
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2.5k
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Heatmap only including DE genes?
heatmap coolmap pheatmap
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
4
votes
6
replies
18k
views
R studio input style for generating heatmap (RNAseq)
heatmap r studio log2foldchange
updated 4.2 years ago by ★ 13k • written 4.2 years ago by • 0
0
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3
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685
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how to draw multiple heatmap from GeneOverlap
GeneOverlap multiple figures heatmap
updated 4.2 years ago by 65k • written 4.2 years ago by ▴ 140
0
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6
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1.7k
views
Breaking down the output from plotEigengeneNetworks()
WGCNA Heatmap EigenGeneNetworks
4.5 years ago l.s.wijaya • 0
1
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2
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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
3
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7
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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 ▴ 260 • written 4.6 years ago by ▴ 10
0
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2
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1.2k
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a newbie question on ConsensusClusterPlus
consensusclusterplus heatmap
4.7 years ago niki.nowhere • 0
0
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2
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4.0k
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Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by • 0
2
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3
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1.6k
views
RNAseq and heatmap
deseq2 RNA-seq Heatmap
updated 4.8 years ago by 41k • written 4.8 years ago by ▴ 10
2
votes
8
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3.3k
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
0
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0
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1.9k
views
Adjusting the size of the visual output from cluster profiler
clusterProfiler heatmap GOAnalysis
4.9 years ago anthony.nash ▴ 20
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0
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1.3k
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Clustering large dataset
HeatMap Cairo Graphics Device Failed to create Cairo backend seqplots
updated 5.1 years ago by 3.8k • written 5.1 years ago by ▴ 450
1
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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
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0
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635
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Superheat adjusting making left label size
r R heatmap
5.3 years ago coyoung ▴ 10
0
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1
reply
1.3k
views
SC3 how to customize plots ?
SC3 plot consensus marker heatmap
updated 5.4 years ago by ▴ 150 • written 5.4 years ago by • 0
4
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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
1
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2
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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
0
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1
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1.0k
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PureCN Solution Heatmap values
PureCN heatmap likelihoods
5.6 years ago twtoal ▴ 10
0
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4
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1.3k
views
PureCN optimum solution vs heat map
PureCN Solution Heatmap
updated 5.7 years ago by ▴ 130 • written 5.7 years ago by ▴ 10
7
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6
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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
1
vote
1
reply
954
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by • 0
3
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5
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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
1
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1
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1.1k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
0
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1
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1.4k
views
How to control the size of labels on heatmaps in DiffBind
diffbind labels heatmap
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
2
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2
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1.1k
views
Problem with using `GRheatmapData` function in compEpiTools package
compEpiTools error heatmap
updated 6.6 years ago by ▴ 200 • written 6.6 years ago by • 0
0
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1
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1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 6.6 years ago by ★ 13k • written 6.6 years ago by • 0
0
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1
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1.2k
views
How to generate heatmap for three groups
rnaseq ruvseq heatmap
updated 6.8 years ago by 65k • written 6.8 years ago by • 0
0
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1
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2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2 tpm heatmap pheatmap
updated 6.9 years ago by 41k • written 6.9 years ago by ▴ 40
0
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2
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4.8k
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DESeq2: how to interpret the heatmap clustering samples
deseq2 rlog transformation heatmap scale
7.1 years ago lina.faller ▴ 10
0
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0
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1.8k
views
use control_condition in heatmap with cummeRbund
cummerbund heatmap
7.1 years ago domenico.somma • 0
6
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3
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6.9k
views
Heatmap Plotting in R
heatmap R bioconductor
8.8 years ago • updated 7.1 years ago Deepak Tanwar ▴ 10
0
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0
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1.5k
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cummeRbund heatmap for specific isoforms (not genes)
cummerbund heatmap isoforms transcript_id
7.1 years ago domenico.somma • 0
1
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2
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2.0k
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Diffbind: how to include all the samples in the heatmap while using the contrast
diffbind heatmap correlation
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by • 0
0
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1
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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 65k • written 7.1 years ago by • 0
2
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7
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4.9k
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Heatmap of a subset of genes
heatmap
written 8.0 years ago by ▴ 40
2
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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
0
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0
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6.4k
views
Pheatmap: how to use breaks for pheatmap
pheatmap heatmap
7.5 years ago jarod_v6@libero.it ▴ 40
1
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4
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1.3k
views
Methylation profile through chromosome
R heatmap
7.7 years ago Adam • 0
2
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1
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1.5k
views
DiffBind affinity vs occupancy Heatmaps
diffbind heatmap pearsoncorrelation
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by ▴ 10
0
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8
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1.4k
views
Regarding general understanding of DiffBind
diffbind heatmap
7.8 years ago shubhibartaria ▴ 10
5
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2
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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
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5
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1.7k
views
What color is assigned in heatmap for time series analysis
deseq2 time course heatmap
updated 7.9 years ago by ▴ 10 • written 7.9 years ago by ▴ 10
1
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3
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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
2
replies
977
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
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
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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