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MLP

Mean Log P Analysis


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews GO, GeneExpression, Genetics, KEGG, Pathways, Reactome, Software
Version 1.50.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL-3
Depends
Imports AnnotationDbi, gplots, graphics, stats, utils
System Requirements
URL
See More
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
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Package Archives

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

Source Package MLP_1.50.0.tar.gz
Windows Binary MLP_1.50.0.zip
macOS Binary (x86_64) MLP_1.50.0.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