POMA

DOI: 10.18129/B9.bioc.POMA    

This is the development version of POMA; for the stable release version, see POMA.

User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

Bioconductor version: Development (3.13)

POMA introduces a structured, reproducible and easy-to-use workflow for the visualization, pre-processing, exploratory and statistical analysis of mass spectrometry data. The main aim of POMA is to enable a flexible data cleaning and statistical analysis processes in one comprehensible and user-friendly R package. This package also has a Shiny app version that implements all POMA functions. See https://github.com/pcastellanoescuder/POMAShiny.

Author: Pol Castellano-Escuder [aut, cre] , Raúl González-Domínguez [aut] , Cristina Andrés-Lacueva [aut] , Alex Sánchez-Pla [aut]

Maintainer: Pol Castellano-Escuder <polcaes at gmail.com>

Citation (from within R, enter citation("POMA")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("POMA")

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("POMA")

 

HTML R Script POMA EDA Example
HTML R Script POMA Normalization Methods
HTML R Script POMA Workflow
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Metabolomics, Normalization, Preprocessing, Proteomics, ReportWriting, Software, Visualization
Version 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports Biobase, broom, caret, clisymbols, ComplexHeatmap, crayon, dplyr, e1071, ggcorrplot, ggplot2, ggraph, ggrepel, glasso (>= 1.11), glmnet, impute, knitr, limma, magrittr, mixOmics, MSnbase(>= 2.12), patchwork, plotly, qpdf, randomForest, RankProd(>= 3.14), reshape2, rmarkdown, tibble, tidyr, vegan
LinkingTo
Suggests BiocStyle, covr, tidyverse, testthat (>= 2.3.2)
SystemRequirements
Enhances
URL https://github.com/pcastellanoescuder/POMA
BugReports https://github.com/pcastellanoescuder/POMA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package POMA_1.1.0.tar.gz
Windows Binary POMA_1.1.0.zip
macOS 10.13 (High Sierra) POMA_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/POMA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/POMA
Package Short Url https://bioconductor.org/packages/POMA/
Package Downloads Report Download Stats

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