README.md

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

QCnormSE

The QCnormSE package provides implementations of several quality control procedures and processing steps for normalized gene expression data sets from microarray and RNA-seq experiments in a common framework.

Installation

First install the dependencies from CRAN:

## install CRAN dependencies
cran.dep = c("aplpack",
             "caret",
             "circlize",
             "GGally",
             "ggplot2",
             "ggplotify",
             "ggpubr",
             "Hmisc",
             "tidyr")

cran.dep.to.install = setdiff(cran.dep,
                     installed.packages()[, "Package"])

if (length(cran.dep.to.install) > 0) {
    install.packages(cran.dep.to.install)
}

Next install the dependencies from Bioconductor:

## install Bioconductor dependencies
bioc.dep = c("affyio",
             "BiocGenerics",
             "ComplexHeatmap",
             "edgeR",
             "doppelgangR",
             "GEOquery",
             "illuminaio",
             "recount",
             "S4Vectors",
             "SummarizedExperiment")

bioc.dep.to.install = setdiff(bioc.dep,
                              installed.packages()[, "Package"])

if (length(bioc.dep.to.install) > 0) {
    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

    BiocManager::install(bioc.dep.to.install)
}

Then install the most recent version of QCnormSE from GitHub:

library(devtools)
install_github("szymczak-lab/QCnormSE")

Usage

A detailed user guide is available as vignette.

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.