Package: MLP 1.61.0

Tobias Verbeke

MLP: Mean Log P Analysis

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.

Authors: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]

MLP_1.61.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MLP/json (API)

# Install 'MLP' in R:

install.packages('MLP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:MLP-1.61.0(bioc 3.24)MLP-1.60.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genetics geneexpression pathways reactome kegg go

4.82 score 1 packages 11 scripts 592 downloads 37 mentions 6 exports 40 dependencies

Last updated from:14fdc6f434. Checks:8 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	338
linux-devel-x86_64	ERROR	788
source / vignettes	OK	389
linux-release-x86_64	ERROR	797
macos-release-arm64	ERROR	646
macos-oldrel-arm64	ERROR	517
windows-devel	ERROR	643
windows-release	ERROR	666
windows-oldrel	ERROR	669
wasm-release	OK	302

Exports:addGeneSetDescription getGeneSets MLP mlpBarplot plotGeneSetSignificance plotGOgraph

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 bitops blob cachem caTools cli cpp11 crayon curl DBI fastmap generics glue gplots gtools httr IRanges jsonlite KEGGREST KernSmooth lifecycle memoise mime openssl pkgconfig png R6 rlang RSQLite S4Vectors Seqinfo sys vctrs XVector

UsingMLP

Introduction | Example Use | References

Rendered fromUsingMLP.Rnwusingutils::Sweave

Last update: 2021-11-19
Started: 2013-11-01

Help page	Topics
Utility function which adds the biological description of the gene sets as a column to the return value of the MLP function (data frame)	addGeneSetDescription
Prepare Pathway Data for the MLP Function	getGeneSets
This function calculates p-values for each gene set based on row permutations of the gene p values or column permutations of the expression matrix; the p values can be obtained either as individual gene set p values or p values based on smoothing across gene sets of similar size.	MLP
Draw a Barplot for MLP Results	mlpBarplot
Plot the Results of an MLP Run	plot.MLP
Plot the Significance for the Genes of a Given Gene Set	plotGeneSetSignificance
Graphical Representation of GO Based MLP Results	plotGOgraph

Package: MLP 1.61.0

MLP: Mean Log P Analysis

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Help Manual

Usage by other packages (reverse dependencies)