ADAM

DOI: 10.18129/B9.bioc.ADAM    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ADAM.

ADAM: Activity and Diversity Analysis Module

Bioconductor version: 3.9

ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes).

Author: André Luiz Molan <andre.molan at unesp.br>, Giordano Bruno Sanches Seco <giordano.bruno at unesp.br>, Agnes Alessandra Sekijima Takeda <agnes.takeda at unesp.br>, Jose Luiz Rybarczyk Filho <jose.luiz at unesp.br>

Maintainer: Jose Luiz Rybarczyk Filho <jose.luiz at unesp.br>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("ADAM")

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("ADAM")

 

HTML	R Script	Using ADAM
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneSetEnrichment, KEGG, Pathways, Software
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL (>= 2)
Depends	R (>= 3.5), stats, utils, methods
Imports	Rcpp (>= 0.12.18), GO.db(>= 3.6.0), KEGGREST(>= 1.20.2), knitr, pbapply (>= 1.3-4), dplyr (>= 0.7.6), DT (>= 0.4), stringr (>= 1.3.1), SummarizedExperiment(>= 1.10.1)
LinkingTo	Rcpp
Suggests	testthat
SystemRequirements	C++11
Enhances
URL
Depends On Me	ADAMgui
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ADAM_1.0.0.tar.gz
Windows Binary	ADAM_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	ADAM_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ADAM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ADAM
Package Short Url	https://bioconductor.org/packages/ADAM/
Package Downloads Report	Download Stats