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>
citation("ADAM")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Using ADAM | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSetEnrichment, KEGG, Pathways, Software |
| Version | 1.0.0 |
| 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 |
| URL |
See More
| Suggests | testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | ADAMgui |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ADAM/ |
| Package Short Url | https://bioconductor.org/packages/ADAM/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |