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https://github.com/ConesaLab/MultiBaC

Single and multiomic batch effect correction
https://github.com/ConesaLab/MultiBaC

Last synced: 27 days ago
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Single and multiomic batch effect correction

Host: GitHub
URL: https://github.com/ConesaLab/MultiBaC
Owner: ConesaLab
Created: 2020-01-31T11:43:34.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2022-01-21T10:30:27.000Z (over 2 years ago)
Last Synced: 2024-02-24T08:32:11.183Z (4 months ago)
Language: R
Homepage:
Size: 5.75 MB
Stars: 5
Watchers: 4
Forks: 2
Open Issues: 5
Metadata Files:
- Readme: README.md

Lists

awesome-multi-omics - MultiBaC - Ugidos - [MultiBaC: A strategy to remove batch effects between different omic data types](https://doi.org/10.1177/0962280220907365) and [R package publication](https://doi.org/10.1093/bioinformatics/btac132) (Batch effect correction / Multi-omics simulation)

README

        # MultiBaC R package repository

[![download](http://www.bioconductor.org/shields/downloads/release/MultiBaC.svg)](https://bioconductor.org/packages/stats/bioc/MultiBaC)

[![](https://img.shields.io/github/last-commit/ConesaLab/MultiBaC.svg)](https://github.com/ConesaLab/MultiBaC/commits/master)

[![dependencies](http://bioconductor.org/shields/dependencies/release/MultiBaC.svg)](http://bioconductor.org/packages/release/bioc/html/MultiBaC.html#since)

This repository contains the `R` package [now hosted on

Bioconductor](http://bioconductor.org/packages/release/bioc/html/MultiBaC.html)

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](http://www.bioconductor.org/packages/release/bioc/vignettes/MultiBaC/inst/doc/MultiBaC.html)

## Installation

**(Mac OS Users Only:)** Ensure you have installed

[XQuartz](https://www.xquartz.org/) first.

Make sure you have the latest R version and the latest `BiocManager`

package installed following [these

instructions](https://www.bioconductor.org/install/) (if you use legacy

R versions (\<=3.5.0) refer to the instructions at the end of the

mentioned page).

``` r

## 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:

```r

## install MultiBaC

BiocManager::install('MultiBaC')

```

#### `GitHub` Versions

MultiBaC can be also directly installed from this repository:

```r

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\!):

. 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.