MLP

Mean Log P Analysis

Bioconductor version: Release (3.20)

Pathway analysis based on p-values associated to genes from a genes expression analysis of interest. Utility functions enable to extract pathways from the Gene Ontology Biological Process (GOBP), Molecular Function (GOMF) and Cellular Component (GOCC), Kyoto Encyclopedia of Genes of Genomes (KEGG) and Reactome databases. Methodology, and helper functions to display the results as a table, barplot of pathway significance, Gene Ontology graph and pathway significance are available.

Author: Nandini Raghavan [aut], Tobias Verbeke [aut], An De Bondt [aut], Javier Cabrera [ctb], Dhammika Amaratunga [ctb], Tine Casneuf [ctb], Willem Ligtenberg [ctb], Laure Cougnaud [cre], Katarzyna Gorczak [ctb]

Maintainer: Tobias Verbeke <tobias.verbeke at openanalytics.eu>

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

Installation

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


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

BiocManager::install("MLP")

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("MLP")

UsingMLP	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GO, GeneExpression, Genetics, KEGG, Pathways, Reactome, Software
Version	1.54.0
In Bioconductor since	BioC 2.8 (R-2.13) (13.5 years)
License	GPL-3
Depends
Imports	AnnotationDbi, gplots, graphics, stats, utils
System Requirements
URL

Suggests	GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db
Linking To
Enhances
Depends On Me
Imports Me	esetVis
Suggests Me	a4
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MLP_1.54.0.tar.gz
Windows Binary (x86_64)	MLP_1.54.0.zip
macOS Binary (x86_64)	MLP_1.54.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MLP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MLP
Bioc Package Browser	https://code.bioconductor.org/browse/MLP/
Package Short Url	https://bioconductor.org/packages/MLP/
Package Downloads Report	Download Stats