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MultiBaC R package repository

download dependencies

This repository contains the R package now hosted on Bioconductor and our current GitHub version. A comprehensive user's guide can be found at http://www.bioconductor.org/packages/release/bioc/vignettes/MultiBaC/inst/doc/MultiBaC.html

Installation

(Mac OS Users Only:) Ensure you have installed XQuartz first.

Make sure you have the latest R version and the latest BiocManager package installed following these instructions (if you use legacy R versions (<=3.5.0) refer to the instructions at the end of the mentioned page).

## install BiocManager if not installed
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
## ensure the following returns TRUE, or follow guidelines
BiocManager::valid()

Latest Bioconductor Release

You can then install MultiBaC using the following code:

## install MultiBaC
BiocManager::install('MultiBaC')

GitHub Versions

MultiBaC can be also directly installed from this repository:

install.packages("devtools")
devtools::install_github("ConesaLab/MultiBaC")

Contribution

Bug reports and pull requests

To report a bug (or offer a solution for a bug!): https://github.com/ConesaLab/MultiBaC/issues. We fully welcome and appreciate well-formatted and detailed pull requests. Preferrably with tests on our datasets.

Citation

[1] Ugidos, M., Tarazona, S., Prats-Montalbán, J. M., Ferrer, A., & Conesa, A. (2020). MultiBaC: A strategy to remove batch effects between different omic data types. Statistical Methods in Medical Research. https://doi.org/10.1177/0962280220907365 [2] Nueda MJ, Ferrer A, Conesa A. ARSyN: A method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics. 2012;13:553–66.

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Single and multiomic batch effect correction

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