Supplementary materials for the article 'Network hub detection using the entire solution path information'.
See also https://github.com/markkukuismin/MDSD.
install.packages(c("igraph", "ggplot2", "huge", "hglasso", "tidyverse", "gridExtra"))
Package space
package is removed from the CRAN repository (last visit 20/2/2024) and must be installed using the tar.gz file.
Packages DESeq2
and genefilter
are available on Bioconductor,
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("DESeq2", "genefilter"))
Use these scripts to reproduce Figures of the article,
manuscript_figures/Fig1.R
: Main article Figure 1.manuscript_figures/Supp_Fig2_and_Fig3.R
: Main article Figure 2.real_data_examples/Maize_ligule/Maize_ligule_hglasso.R
: Main article Figure 3.
Use these scripts to reproduce the simulations results reported in the main article and Supplementary materials,
simulations/simulations_lossy_screening.R
: Lossy screening rule of the sample correlation matrix simulations.simulations/simulations_hglasso.R
: Hub glasso simulations.simulations/simulations_local_hub_screening.R
: Firouzi & Hero (2013) hub screening method simulations.simulations/simulations_space.R
: space simulations.
Use the script to reproduce the real data example reported in the main article. The data set is publicly available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61333
Maize_ligule_hglasso.R
: Derive a gene co-expression network to detect hub genes of Maize ligule data.