MKomics   MKomics

The repository includes the development version of R package MKomics

License: LGPL v3 Project Status: Active – The project has reached a stable, usable state and is being actively developed. CRAN_Status_Badge cran checks

Description

Similarity plots based on correlation and median absolute deviation (MAD); adjusting colors for heatmaps; aggregate technical replicates; calculate pairwise fold-changes and log fold-changes; computate one- and two-way ANOVA; simplified interface to package 'limma' (Ritchie et al. (2015), doi:10.1093/nar/gkv007) for moderated t-test and one-way ANOVA; Hamming and the Levenshtein (edit) distance of strings as well as optimal alignment scores for global (Needleman-Wunsch) and local (Smith-Waterman) alignments with constant gap penalties (Merkl and Waack (2009), ISBN:978-3-527-32594-8).

Installation

The package requires Bioconductor packages limma and ComplexHeatmap, which can be installed via

## Install package BiocManager
install.packages("BiocManager")
## Use BiocManager to install limma
BiocManager::install("limma")
## Use BiocManager to install ComplexHeatmap
BiocManager::install("ComplexHeatmap")

For the installation of package MKomics use

## Installation of CRAN version
install.packages("MKomics")

## Development version from GitHub
# install.packages("remotes")
remotes::install_github("stamats/MKomics")

Getting started

library(MKomics)