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POMA

Tools for Omics Data Analysis


Bioconductor version: Release (3.18)

A reproducible and easy-to-use toolkit for visualization, pre-processing, exploration, and statistical analysis of omics datasets. 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 has a Shiny app version called POMAShiny that implements all POMA functions. See https://github.com/pcastellanoescuder/POMAShiny. See Castellano-Escuder P, González-Domínguez R, Carmona-Pontaque F, et al. (2021) for more details.

Author: Pol Castellano-Escuder [aut, cre]

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

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

Installation

To install this package, start R (version "4.3") and enter:


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

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

Details

biocViews BatchEffect, Classification, Clustering, DecisionTree, DimensionReduction, MultidimensionalScaling, Normalization, Preprocessing, PrincipalComponent, RNASeq, Regression, Software, StatisticalMethod, Visualization
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
Imports broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, ggplot2, ggrepel, glasso (>= 1.11), glmnet, impute, limma, magrittr, mixOmics, randomForest, RankProd(>= 3.14), rmarkdown, SummarizedExperiment, tibble, tidyr, uwot, vegan
System Requirements
URL https://github.com/pcastellanoescuder/POMA
Bug Reports https://github.com/pcastellanoescuder/POMA/issues
See More
Suggests BiocStyle, covr, ggraph, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me fobitools
Links To Me
Build Report Build Report

Package Archives

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

Source Package POMA_1.12.0.tar.gz
Windows Binary POMA_1.12.0.zip
macOS Binary (x86_64) POMA_1.12.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/POMA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/POMA
Bioc Package Browser https://code.bioconductor.org/browse/POMA/
Package Short Url https://bioconductor.org/packages/POMA/
Package Downloads Report Download Stats