Question: Tool that can split genes into groups with similar expression pattern overtime and plot them?
1
gravatar for salamandra
22 months ago by
salamandra310
salamandra310 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 • 753 views
ADD COMMENTlink modified 22 months ago by exin50 • written 22 months ago by salamandra310

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

ADD REPLYlink modified 22 months ago • written 22 months ago by cpad011213k

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 22 months ago by salamandra310

Use clustering methods

ADD REPLYlink written 22 months ago by cpad011213k

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 22 months ago by salamandra310

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

ADD REPLYlink modified 22 months ago • written 22 months ago by cpad011213k
2
gravatar for exin
22 months 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 22 months ago • written 22 months ago by exin50

thank you very much!

ADD REPLYlink written 22 months ago by salamandra310
1
gravatar for btsui
22 months ago by
btsui290
UCSD
btsui290 wrote:

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

enter image description here

ADD COMMENTlink modified 22 months ago • written 22 months ago by btsui290
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