PAA
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see PAA.
PAA (Protein Array Analyzer)
Bioconductor version: 3.10
PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.
Author: Michael Turewicz [aut, cre], Martin Eisenacher [ctb, cre]
Maintainer: Michael Turewicz <michael.turewicz at rub.de>, Martin Eisenacher <martin.eisenacher at rub.de>
citation("PAA")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PAA")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PAA")| PAA tutorial | R Script | |
| PAA_1.7.1.pdf | ||
| Reference Manual | ||
| README | Text | |
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Microarray, OneChannel, Proteomics, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | BSD_3_clause + file LICENSE |
| Depends | R (>= 3.2.0), Rcpp (>= 0.11.6) |
| Imports | e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva |
| System Requirements | C++ software package Random Jungle |
| URL | http://www.ruhr-uni-bochum.de/mpc/software/PAA/ |
See More
| Suggests | BiocStyle, RUnit, BiocGenerics, vsn |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PAA_1.20.0.tar.gz |
| Windows Binary | PAA_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | PAA_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PAA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PAA |
| Bioc Package Browser | https://code.bioconductor.org/browse/PAA/ |
| Package Short Url | https://bioconductor.org/packages/PAA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |