Bioconductor - BloodGen3Module

Bioconductor - BloodGen3Module
Bioconductor 3.22
Software Packages
BloodGen3Module
BloodGen3Module
This is the
released
version of BloodGen3Module; for the devel version, see
BloodGen3Module
This R package for performing module repertoire analyses and generating fingerprint representations
DOI:
10.18129/B9.bioc.BloodGen3Module
Bioconductor version:
Release (3.22)
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]
ORCID: 0000-0001-8851-7730
Maintainer:
Darawan Rinchai
Citation (from within R, enter
citation("BloodGen3Module")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

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")
BloodGen3Module: Modular Repertoire Analysis and Visualization
HTML
R Script
Reference Manual
PDF
NEWS
Text
LICENSE
Text
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Details
biocViews
GeneExpression
Software
Visualization
Version
1.18.0
In Bioconductor since
BioC 3.13 (R-4.1) (5 years)
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
System Requirements
URL
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Suggests
RUnit
devtools
BiocGenerics
knitr
rmarkdown
Linking To
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Depends On Me
Imports Me
Suggests Me
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Build Report
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Installation
instructions to use this package in your R session.
Source Package
BloodGen3Module_1.18.0.tar.gz
Windows Binary (x86_64)
BloodGen3Module_1.18.0.zip
(64-bit only)
macOS Binary (x86_64)
BloodGen3Module_1.18.0.tgz
macOS Binary (arm64)
BloodGen3Module_1.18.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/BloodGen3Module
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/BloodGen3Module
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