MOSClip

This is the released version of MOSClip; for the devel version, see MOSClip.

Multi Omics Survival Clip

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DOI: 10.18129/B9.bioc.MOSClip

Bioconductor version: Release (3.22)

Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.

Author: Paolo Martini [aut, cre] ORCID iD ORCID: 0000-0002-0146-1031 , Anna Bortolato [aut] ORCID iD ORCID: 0009-0009-9327-6084 , Anna Tanada [aut] ORCID iD ORCID: 0000-0003-3224-0538 , Enrica Calura [aut] ORCID iD ORCID: 0000-0001-8463-2432 , Stefania Pirrotta [aut] ORCID iD ORCID: 0009-0004-0030-217X , Federico Agostinis [aut]

Maintainer: Paolo Martini <paolo.martini at unibs.it>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("MOSClip")

MOSClip HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, GraphAndNetwork, Pathways, Reactome, Regression, Software, StatisticalMethod, Survival

Version 1.4.0

In Bioconductor since BioC 3.20 (R-4.4) (1 year)

License AGPL-3

Depends R (>= 4.4.0)

Imports MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix

System Requirements

URL https://github.com/CaluraLab/MOSClip/

Bug Reports https://github.com/CaluraLab/MOSClip/issues

Suggests RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0)

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Package Archives

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

Source Package MOSClip_1.4.0.tar.gz

Windows Binary (x86_64) MOSClip_1.3.2.zip

macOS Binary (x86_64) MOSClip_1.4.0.tgz

macOS Binary (arm64) MOSClip_1.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/MOSClip

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MOSClip

Bioc Package Browser https://code.bioconductor.org/browse/MOSClip/

Package Short Url https://bioconductor.org/packages/MOSClip/

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