This network propagation based method (NP-method), which takes advantage of the global network differential information, carries out a integrated random walk plus forward searching algorithm to infer the perturbed miRNAs as well as their leading-edge target genes.
The lastest release is programmed with R language.
Scripts can be downloaded here.
Supporting and test data can be downloaded here.
See details in README.
Step 1: precalculate M matrix using precalculate_M.R
Step 2: get foreground NPESs for miRNAs using NP.fg.R
Step 3: get background NPES distributions for miRNAs using NP.bg.R
Step 4: normalize NPESs and get p-values for miRNAs using NP.pvalue.R
Please feel free to contact us when you have questions.
Ting Wang (firstname.lastname@example.org)
or Jin Gu (email@example.com)