MOSClip

This is the development version of MOSClip; for the stable release version, see MOSClip.

Multi Omics Survival Clip

Bioconductor version: Development (3.21)

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: ), Anna Bortolato [aut] (ORCID: ), Anna Tanada [aut] (ORCID: ), Enrica Calura [aut] (ORCID: ), Stefania Pirrotta [aut] (ORCID: ), 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.1.0
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
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)
Linking To
Enhances
Depends On Me
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	MOSClip_1.1.0.tar.gz
Windows Binary (x86_64)	MOSClip_1.1.0.zip
macOS Binary (x86_64)	MOSClip_1.1.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MOSClip
Source Repository (Developer Access)	git clone [email protected]:packages/MOSClip
Bioc Package Browser	https://code.bioconductor.org/browse/MOSClip/
Package Short Url	https://bioconductor.org/packages/MOSClip/
Package Downloads Report	Download Stats