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NEArender (version 1.5)

Network Enrichment Analysis

Description

Performs network enrichment analysis against functional gene sets. Benchmarks networks. Renders raw gene profile matrices of dimensionality "N genes x N samples" into the space of gene set (typically pathway) enrichment scores of dimensionality "N pathways x N samples".

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Version

Install

install.packages('NEArender')

Monthly Downloads

2

Version

1.5

License

GPL-3

Maintainer

Ashwini Jeggari

Last Published

March 21st, 2018

Functions in NEArender (1.5)

import.gs

Read in an AGS or FGS test file
benchmark

Benchmark networks using Network Enrichment Analysis (NEA)
can.sig.go

Example functional gene sets (FGS) from GO and KEGG
connectivity

Connectivity
import.net

Import a network text file
mutations2ags

Create AGS from a mutation matrix
fantom5.43samples

A Fantom5 transcriptomes in 43 carincinoma cell samples
char2int.fast

char2int function
roc

ROC for NEA benchmarks
samples2ags

Create AGS from a raw data matrix.
gsea.render

Gene Set Enrichment Analysis (GSEA)
save_gs_list

Create a TAB-delimited text file from AGS or FGS
tcga.gbm

NEArender
as_genes_fgs

Create single-gene FGS
topology2nd

Higher order topology and correlation between node degrees
set.heat

Plot a heatmap of NEA/GSEA output
nea.render

Network Enrichment Analysis (NEA)
net.kegg

A more compact alternative global network for the network enrichment analysis