Pathway analysis via network smoothing R package.
On Windows, you should have Rtools.
Install PANTS
from GitHub using remotes
within R. You must install remotes
, e.g. with install.packages("remotes")
, if you haven't before. PANTS
depends on ezlimma
, which depends on limma
, so you must also install these if you haven't before.
#if haven't already installed limma
install.packages("BiocManager") #if haven't already installed BiocManager
library(BiocManager)
BiocManager::install("limma")
library(remotes)
remotes::install_github(repo="jdreyf/ezlimma", build_opts = c("--no-resave-data", "--no-manual"))
remotes::install_github(repo="jdreyf/PANTS", build_opts = c("--no-resave-data", "--no-manual"))
If you receive Error: Dependency package(s) A, B, C not available
, you can install these packages using install.packages()
as above.
The vignette presents a tutorial. To see the vignette:
library(limma)
library(ezlimma)
library(PANTS)
browseVignettes(package="PANTS")
and click on HTML.