PIMENTo

PIMENTo is an R package to normalize, analyze, and visualize microarray data

Native R Installation

You can install PIMENTo using devtools and BiocManager:

# Install Dependencies from CRAN
install.packages(c('devtools', 'BiocManager'), repos='https://cloud.r-project.org/')

# Install Dependencies from Bioconductor
BiocManager::install(c('impute', 'DESeq2', 'affy', 'limma'))

# Install PIMENTo
devtools::install_github("HardimanLab/PIMENTo")

# Load package
library(PIMENTo)

Run PIMENTo with Docker

To start an interactive PIMENTo session and mount the current
working directory, $PWD, within the Docker container to /home/pimento/
Run the following:

docker run -v "$PWD:/home/pimento/" --rm -it hardimanlab/pimento

_{Note that the --rm flag means that the container will autoremove
after you close the PIMENTo session.}

Links

PIMENTo - GitHub
PIMENTo - DockerHub