BloodGen3Module

DOI: 10.18129/B9.bioc.BloodGen3Module    

This is the development version of BloodGen3Module; for the stable release version, see BloodGen3Module.

This R package for performing module repertoire analyses and generating fingerprint representations

Bioconductor version: Development (3.15)

The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows.

Author: Darawan Rinchai [aut, cre]

Maintainer: Darawan Rinchai <drinchai at gmail.com>

Citation (from within R, enter citation("BloodGen3Module")):

Installation

To install this package, start R (version "4.2") and enter:

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

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

BiocManager::install("BloodGen3Module")

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("BloodGen3Module")

 

HTML R Script BloodGen3Module: Modular Repertoire Analysis and Visualization
PDF   Reference Manual

Details

biocViews GeneExpression, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License GPL-2
Depends R (>= 4.1)
Imports SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma
LinkingTo
Suggests RUnit, devtools, BiocGenerics, knitr, rmarkdown
SystemRequirements
Enhances
URL
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 BloodGen3Module_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/BloodGen3Module
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BloodGen3Module
Package Short Url https://bioconductor.org/packages/BloodGen3Module/
Package Downloads Report Download Stats

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