NEArender: Network Enrichment Analysis

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'.

Author
Andrey Alexeyenko [aut, cph, ths], Ashwini Jeggari [aut, cre]
Date of publication
2016-08-25 18:08:24
Maintainer
Ashwini Jeggari <ashwinipriya.jeggari@ki.se>
License
GPL-3
Version
1.4

View on CRAN

Man pages

as_genes_fgs
Create single-gene FGS
benchmark
Benchmark networks using Network Enrichment Analysis (NEA)
can.sig.go
Example functional gene sets (FGS) from GO and KEGG
char2int
char2int function
connectivity
Node degree distribution and network scale-freeness
fantom5.43samples
A Fantom5 transcriptomes in 43 carincinoma cell samples
gsea.render
Gene Set Enrichment Analysis (GSEA)
import.gs
Read in an AGS or FGS test file
import.net
Import a network text file
mutations2ags
Create AGS from a mutation matrix
nea.render
Network Enrichment Analysis (NEA)
net.kegg
A more compact alternative global network for the network...
roc
ROC for NEA benchmarks
samples2ags
Create AGS from a raw data matrix.
save_gs_list
Create a TAB-delimited text file from AGS or FGS
set.heat
Plot a heatmap of NEA/GSEA output
tcga.gbm
NEArender
topology2nd
Higher order topology and correlation between node degrees

Files in this package

NEArender
NEArender/inst
NEArender/inst/doc
NEArender/inst/doc/NEArender_vignette.R
NEArender/inst/doc/NEArender_vignette.Rmd
NEArender/inst/doc/NEArender_vignette.pdf
NEArender/NAMESPACE
NEArender/data
NEArender/data/can.sig.go.RData
NEArender/data/net.kegg.RData
NEArender/data/fantom5.43samples.RData
NEArender/data/datalist
NEArender/data/tcga.gbm.RData
NEArender/R
NEArender/R/gsea-render.r
NEArender/R/connectivity.r
NEArender/R/benchmark.r
NEArender/R/save_gs_list.r
NEArender/R/sample2ags.r
NEArender/R/as-genes-fgs.r
NEArender/R/roc.r
NEArender/R/mutations2ags.r
NEArender/R/nea-data.r
NEArender/R/topology2nd.r
NEArender/R/nea-render.r
NEArender/R/import-net.r
NEArender/R/import-gs.r
NEArender/R/heatplot.r
NEArender/R/char2int.r
NEArender/vignettes
NEArender/vignettes/NEArender_vignette.Rmd
NEArender/MD5
NEArender/build
NEArender/build/vignette.rds
NEArender/DESCRIPTION
NEArender/man
NEArender/man/as_genes_fgs.Rd
NEArender/man/fantom5.43samples.Rd
NEArender/man/net.kegg.Rd
NEArender/man/benchmark.Rd
NEArender/man/save_gs_list.Rd
NEArender/man/connectivity.Rd
NEArender/man/import.gs.Rd
NEArender/man/can.sig.go.Rd
NEArender/man/nea.render.Rd
NEArender/man/tcga.gbm.Rd
NEArender/man/samples2ags.Rd
NEArender/man/topology2nd.Rd
NEArender/man/gsea.render.Rd
NEArender/man/mutations2ags.Rd
NEArender/man/char2int.Rd
NEArender/man/roc.Rd
NEArender/man/set.heat.Rd
NEArender/man/import.net.Rd