ADAM

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

ADAM: Activity and Diversity Analysis Module

Bioconductor version: Development (3.24)

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 [aut], Giordano Bruno Sanches Seco [ctb], Agnes Takeda [ctb], Jose Rybarczyk Filho [ctb, cre, ths]

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

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

André Luiz Molan. ADAM: ADAM: Activity and Diversity Analysis Module. doi:10.18129/B9.bioc.ADAM, R package version 1.29.0, https://bioconductor.org/packages/ADAM.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

"Using ADAM"	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Software
Version	1.29.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
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)
System Requirements	C++11
URL

Suggests	testthat, rmarkdown, BiocStyle
Linking To	Rcpp
Enhances
Depends On Me	ADAMgui
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ADAM_1.29.0.tar.gz
Windows Binary (x86_64)	ADAM_1.29.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	ADAM_1.29.0.tgz
macOS Binary (sonoma-arm64)	ADAM_1.29.0.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