Showing : heatmap.2 • reset
4
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8
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7.9k
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Scaling genes to have unit variance for clustering / heatmaps with DESeq2
deseq2 heatmap.2 bicluster pheatmap
updated 6.5 years ago by 41k • written 8.6 years ago by ▴ 10
1
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2
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10k
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Use of various distance measures and clustering methods in heatmap creation
gplots heatmap.2 bioconductor pearsoncorrelation average
8.8 years ago svlachavas ▴ 830
1
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2
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2.5k
views
R crash when matrix nrows exceeds 45000 using pheatmap/heatmap.2
pheatmap heatmap.2
8.1 years ago John ▴ 30
1
vote
1
reply
506
views
Add 'ColSideColors' using 'heatmap.2' function
ColSideColors heatmaps heatmap.2
updated 13 months ago by ▴ 80 • written 13 months ago by ▴ 10
0
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1
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1.5k
views
Error when trying to plot sample distance from and assay object generated with DESeq2
deseq2 heatmap.2
updated 8.9 years ago by 41k • written 8.9 years ago by ▴ 30
0
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2
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1.4k
views
Possible construction of heatmap for clustering only genes for different treatments and not samples
heatmap.2 clustering common DEG genes bioconductor
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 830
2
votes
2
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3.8k
views
ColSideColors set by rows for heatmap.2 in RStudio
rstudio heatmap.2
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
0
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1
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687
views
collided row names in heatmap.2
heatmap.2 genefilter deseq2
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
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7
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4.9k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
9.1 years ago svlachavas ▴ 830
1
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1
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1.6k
views
heatmap2 error key
heatmap.2
updated 8.0 years ago by 65k • written 8.0 years ago by ▴ 90
1
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5
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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
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3
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2.2k
views
How to combine replicates creating heatmap?
deseq2 edgeR heatmap.2
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 50
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
0
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1
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1.7k
views
heatmap.2 reorder branches
heatmap.2 hclust reorderfun
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 360
8
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1
reply
9.2k
views
extracting the genes associated with the clusters
heatmap.2 pheatmap complexheatmap heatplus
updated 7.2 years ago by ▴ 680 • written 7.2 years ago by ▴ 670
0
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4
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6.5k
views
Sample-to-sample distance matrix using heatmap.2
heatmap.2 gplots DESeq2
6.6 years ago Jane Merlevede ▴ 90
0
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2
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1.2k
views
gene names disapper from heatmap.2 after adding gene descripton
heatmap.2 edger
6.6 years ago mictadlo ▴ 10
5
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3
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12k
views
Interpreting heatmap in DESEQ2
deseq2 heatmap.2
updated 6.1 years ago by ▴ 150 • written 6.1 years ago by • 0
0
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1
reply
796
views
RPKM representation in heatmap is not accurate
heatmap.2 z-score
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
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0
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2.6k
views
heatmap.2() making columns narrower to make them look like microarray?
heatmap.2 pheatmap
8.6 years ago AJC ▴ 10
0
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0
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2.6k
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Problem with the colors in the heatmap.2 function and the color key values range
gplots heatmap.2 affymetrix microarrays color key
8.6 years ago svlachavas ▴ 830
0
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0
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1.6k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
6.2 years ago lawarde.ankita1 ▴ 30
22 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
Sorry, for questions about statistical analysis plan and interpretation of results, I recommend to work with a local statistician or someon…
Answer: Fold change calculation in Diffbind vs. DESEQ2? by Michael Love 41k
There was a recent DiffBind question on the support site that noticed the same thing, try searching recent DiffBind posts.
Answer: Timecourse RNASeq analysis by Michael Love 41k
There are many choices for time course, and we have an example in our workflow (rnaseqGene). Otherwise, I recommend to consult a local …
Answer: Padj "NA" with thousands of low count although the raw read counts are quite lar by Michael Love 41k
You can either turn off independent filtering in `results` or use `ihw` see the vignette.
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Thanks Gordon for a detail guide! You have a great memory of time. GSVA also do differential express at pathway level (https://bioconductor…
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Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
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