Analysis of gene co-expression by network

[EA2106-Universite-Francois-Rabelais]

This pipeline uses an expression matrix produced by microarray or RNA-seq analyses. As a starting point, we provide an expression matrix for Arabidopsis

[sanchari24]

Hello, could you please kindly elaborate the installation process ? I am interested to construct the HRR network from PCC. I navigated to the hrr folder. After that, how do I "compile with mpich by typing 'make' in the directory" ? What are the commands ?

Secondly, I already have the Pearson correlations as a text file with "Node1", "Node2" and "pcc". Can I use that file anywhere? It will save a lot of time to re-calculate the PCC

Thirdly, Any dependencies in UBUNTU? Thanks

[cascoamarillo]

Hi,

Just create this tutorial for myself after dealing with it, under linux with ubuntu20. Maybe a little late for you, but it can help others...it took me some time too.

For "make" hrr:

Download lapack 3.5...I used that version since it is the one mentioned in Makefile

cd lapack-3.5.0

Check make.inc.example file: rename to "make.inc"

Install libs:

make blaslib make cblaslib #this will not work in ver.3.5.0 make lapacklib

if everything OK, go to /lapacke and "make lapacke"

cd lapacke make lapacke

all libs should be in lapack dir (.a) and (.h) in lapack/lapacke/include

edit Makefile in /hrr:

INCLAPACK=~/bin/lapack-3.5.0/lapacke/include/
LIBLAPACK=~/bin/lapack-3.5.0/liblapacke.a ~/bin/lapack-3.5.0/liblapack.a ~/bin/lapack-3.5.0/libtmglib.a 

then make

make

[EA2106-Universite-Francois-Rabelais]

thanks to @cascoamarillo and apologies to @sanchari24 for not answering. The compilation should be fine, just ensure that mpicc is available for compilation to allow MPI.

[Galaxy-228]

Hi, When i run the software, an err showed un as followed:

Thanks so much.