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NEArender (version 1.4)

Network Enrichment Analysis

Description

Performs network enrichment analysis against functional gene sets. Benchmarks networks. Renders raw gene profile matrices of dimensionality 'Ngenes x Nsamples' into the space of gene set (typically pathway) enrichment scores of dimensionality 'Npathways x Nsamples'.

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Version

Install

install.packages('NEArender')

Monthly Downloads

2

Version

1.4

License

GPL-3

Maintainer

Ashwini Jeggari

Last Published

December 5th, 2016

Functions in NEArender (1.4)

as_genes_fgs

Create single-gene FGS
import.net

Import a network text file
char2int

char2int function
fantom5.43samples

A Fantom5 transcriptomes in 43 carincinoma cell samples
can.sig.go

Example functional gene sets (FGS) from GO and KEGG
gsea.render

Gene Set Enrichment Analysis (GSEA)
mutations2ags

Create AGS from a mutation matrix
connectivity

Node degree distribution and network scale-freeness
benchmark

Benchmark networks using Network Enrichment Analysis (NEA)
import.gs

Read in an AGS or FGS test file
save_gs_list

Create a TAB-delimited text file from AGS or FGS
nea.render

Network Enrichment Analysis (NEA)
roc

ROC for NEA benchmarks
set.heat

Plot a heatmap of NEA/GSEA output
samples2ags

Create AGS from a raw data matrix.
net.kegg

A more compact alternative global network for the network enrichment analysis
topology2nd

Higher order topology and correlation between node degrees
tcga.gbm

NEArender