Question: Tool that can split genes into groups with similar expression pattern overtime and plot them?
1
gravatar for salamandra
2.2 years ago by
salamandra330
salamandra330 wrote:

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.

clustering rna-seq • 876 views
ADD COMMENTlink modified 2.2 years ago by exin50 • written 2.2 years ago by salamandra330

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by cpad011214k

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

ADD REPLYlink written 2.2 years ago by salamandra330

Use clustering methods

ADD REPLYlink written 2.2 years ago by cpad011214k

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

ADD REPLYlink written 2.2 years ago by salamandra330

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

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by cpad011214k
2
gravatar for exin
2.2 years ago by
exin50
Australia
exin50 wrote:

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.

Screen_Shot_2018_08_24_at_5_14_54_pm

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by exin50

thank you very much!

ADD REPLYlink written 2.2 years ago by salamandra330
1
gravatar for btsui
2.2 years ago by
btsui290
UCSD
btsui290 wrote:

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

enter image description here

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by btsui290
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