In PadiLab/CRANE: Randomly perturbing networks with fixed strength

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CRANE v1.0.0

Constrained Random Alteration of Network Edges (CRANE) is a computational method for sampling networks with fixed node strengths. This package also include CRANE integraction with ALPACA.

Installation

You can install the released version of CRANE from GitHub with:

library(devtools)
install_github("PadiLab/CRANE")

Publication

Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules
James T Lim, Chen Chen, Adam D Grant, Megha Padi
bioRxiv 2020.07.12.198747; doi: https://doi.org/10.1101/2020.07.12.198747
url: https://www.biorxiv.org/content/10.1101/2020.07.12.198747v1

Examples

We have included network edge list from angiogenic ovarian cancer (ang) and non-angiogenic ovarian cancer (nonAng). The following are some example use:

1. CRANE for network perturbation

library(CRANE)
head(ang)

# Running CRANE for bipartite network
newElist=crane.bipartite(ang,alpha=0.3)

head(newElist)

1. CRANE integration with ALPACA

library(ALPACA)
library(CRANE)

# Create Input Matrix nonAng as the baseline.
input=cbind(nonAng,ang[,3])

# Run ALPACA
alp=alpaca(input,NULL,verbose = F)

# Apply Crane
alpListObject=alpaca.crane(input, alp, isParallel = T)

# TF Results
head(alpListObject$TF)

# Gene Results
head(alpListObject$Gene)

PadiLab/CRANE documentation built on Sept. 19, 2020, 8:28 a.m.