multiSight

DOI: 10.18129/B9.bioc.multiSight    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see multiSight.

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Bioconductor version: 3.15

multiSight is an R package providing functions to analyze your omic datasets in a multi-omics manner based on Stouffer's p-value pooling and multi-block statistical methods. For each omic dataset you furnish, multiSight provides classification models with feature selection you can use as biosignature: (i) To forecast phenotypes (e.g. to diagnostic tasks, histological subtyping), (ii) To design Pathways and gene ontology enrichments (Over Representation Analysis), (iii) To build Network inference linked to PubMed querying to make assumptions easier and data-driven. Main analysis are embedded in an user-friendly graphical interface.

Author: Florian Jeanneret [cre, aut] , Stephane Gazut [aut]

Maintainer: Florian Jeanneret <florian.jeanneret at cea.fr>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("multiSight")

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("multiSight")

 

HTML	R Script	multiSight quick start guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, DifferentialExpression, GeneSetEnrichment, Network, NetworkInference, Pathways, RNASeq, Software, miRNA
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	CeCILL + file LICENSE
Depends	R (>= 4.1)
Imports	golem, config, R6, shiny, shinydashboard, DT, dplyr, stringr, anyLib, caret, biosigner, mixOmics, stats, DESeq2, clusterProfiler, rWikiPathways, ReactomePA, enrichplot, ppcor, metap, infotheo, igraph, networkD3, easyPubMed, utils, htmltools, rmarkdown, ggnewscale
LinkingTo
Suggests	org.Mm.eg.db, rlang, markdown, attempt, processx, testthat, knitr, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/Fjeanneret/multiSight/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	multiSight_1.4.0.tar.gz
Windows Binary	multiSight_1.4.0.zip
macOS Binary (x86_64)	multiSight_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/multiSight
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/multiSight
Package Short Url	https://bioconductor.org/packages/multiSight/
Package Downloads Report	Download Stats