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ADAM

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

ADAM: Activity and Diversity Analysis Module


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("ADAM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Software
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (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
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Suggests testthat, rmarkdown, BiocStyle
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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