Best tools for Visualing RNASeq data
Helloo biostars, I want visualise/plot the expression pattern of a set genes from my RNASeq data. Which are the best R packages or other softawares to do so? I came accross maSigPro and impulseDE but was not impressed by them. Thanks in advance
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Hussain Ather
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Sreeraj Thamban
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You may want to take a look at my answer here, which deals specifically with RNA-seq gene signatures and how best to evaluate them: A: Resources for gene signature creation
If you literally just want to look at patterns of gene expression, then why not use:
heatmap.2 package
complexheatmap package
corrplot
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Kevin Blighe
heatmaps in matplotlib or seaborn might be helpful
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It's unclear what the message is of the plot you want to make. Are you comparing two groups for the expression of one gene?
Hi Coster, I have a group of genes which are involved in a common pathway. I wanted to plot the overall trend of their expression pattern between treated and untreated samples.
Sounds like maybe you want to make an MA plot or a volcano plot? In that case DEseq2 has some built in functions. Otherwise you can make your own MA plot using base R graphics or ggplot.
In addition, for comparing just one gene (or a few) between multiple conditions violin plots are also pretty neat.
Then, i guess, you can overlay the expression pattern (of the the pathway members) over KEGG pathway. There are bioconductor packages to do this.
Why not simply a violin plot log2 fold chages for all genes in that pathway?