Tool that can split genes into groups with similar expression pattern overtime and plot them?

Question

[salamandra]

Does anyone know of a tool that can produce similar plots to 'DegPatterns' function of 'DEGreport' R package? something like this plot? Basically is a plot showing how groups of genes change over time.

Cause I'm having difficulties with DegPatterns.

[cpad0112]

They are boxplots connected by median/mean with CI. In general box plots show median

[salamandra]

Yes, the thing is to know which genes are in the same group. Each plot shows a group of genes with the same behaviour through time

[cpad0112]

Use clustering methods

[salamandra]

You're talking about distance matrix? I know I can use to visualize those groups in a heatmap, but then how to aftwrwards automatically get the list of genes in each group/branch separately? I have a lot of genes so cannot do it manually

[cpad0112]

Ask Kevin nice (as it is weekend). He posted several posts about distance matrices, heat maps, pcas in biostars.

Answer 1

[exin]

Not sure if Mfuzz https://bioconductor.org/packages/release/bioc/html/Mfuzz.html is kind of what you're after? It groups genes by expression patterns, and plot those in the same group together, giving you each group's member genes and "participation scores". Not box plots though.

[salamandra]

thank you very much!

Answer 2

[btsui]

https://seaborn.pydata.org/tutorial/categorical.html