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POMA

Tools for Omics Data Analysis

Bioconductor version: 3.23 · Package version: 1.22.0

The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.

Installation

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

BiocManager::install("POMA")

Details

MaintainerPol Castellano-Escuder <polcaes@gmail.com>
AuthorPol Castellano-Escuder [aut, cre] (ORCID: <https://orcid.org/0000-0001-6466-877X>)
LicenseGPL-3
URLhttps://github.com/pcastellanoescuder/POMA
Bug Reportshttps://github.com/pcastellanoescuder/POMA/issues
Downloads rank374
Source branchRELEASE_3_23
biocViewsBatchEffect, Classification, Clustering, DecisionTree, DimensionReduction, MultidimensionalScaling, Normalization, Preprocessing, PrincipalComponent, RNASeq, Regression, Software, StatisticalMethod, Visualization

Documentation

Download

Dependencies

Depends: R (>= 4.0)

Imports: broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, fgsea, FSA, ggcorrplot, ggplot2, ggrepel, glmnet, grid, impute, janitor, limma, lme4, magrittr, MASS, mixOmics, multcomp, msigdbr, purrr, randomForest, RankProd (>= 3.14), rlang, SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan

Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2)

Reverse dependencies

Imports Me (1): PRONE

Suggests Me (1): fobitools