Tool that can split genes into groups with similar expression pattern overtime and plot them?
2
1
Entering edit mode
2.7 years ago
salamandra ▴ 380

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.

RNA-Seq clustering • 1.1k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

Use clustering methods

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
2.7 years ago
exin ▴ 50

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 COMMENT
0
Entering edit mode

thank you very much!

ADD REPLY
1
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 1471 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6