recipe bioconductor-probatch

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Homepage

https://bioconductor.org/packages/3.12/bioc/html/proBatch.html

License

GPL-3

Recipe

/bioconductor-probatch/meta.yaml

These tools facilitate batch effects analysis and correction in high-throughput experiments. It was developed primarily for mass-spectrometry proteomics (DIA/SWATH), but could also be applicable to most omic data with minor adaptations. The package contains functions for diagnostics (proteome/genome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Non-linear fitting based approaches were also included to deal with complex, mass spectrometry-specific signal drifts.

package bioconductor-probatch

Versions

1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

Depends

• bioconductor-biobase >=2.50.0,<2.51.0

• bioconductor-preprocesscore >=1.52.0,<1.53.0

• bioconductor-pvca >=1.30.0,<1.31.0

• bioconductor-sva >=3.38.0,<3.39.0

• r-base >=4.0,<4.1.0a0

• r-corrplot

• r-data.table

• r-dplyr

• r-ggfortify

• r-ggplot2

• r-lazyeval

• r-lubridate

• r-magrittr

• r-pheatmap

• r-purrr

• r-rcolorbrewer

• r-reshape2

• r-rlang

• r-scales

• r-tibble

• r-tidyr

• r-viridis

• r-wesanderson

• r-wgcna

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-probatch

and update with:

conda update bioconductor-probatch

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-probatch:<tag>

(see bioconductor-probatch/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-probatch/README.html)