timeOmics

DOI: 10.18129/B9.bioc.timeOmics    

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

Time-Course Multi-Omics data integration

Bioconductor version: Development (3.17)

timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.

Author: Antoine Bodein [aut, cre], Olivier Chapleur [aut], Kim-Anh Le Cao [aut], Arnaud Droit [aut]

Maintainer: Antoine Bodein <antoine.bodein.1 at ulaval.ca>

Installation

To install this package, start R (version "4.3") and enter:

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

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

BiocManager::install("timeOmics")

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("timeOmics")

 

HTML	R Script	timeOmics
PDF		Reference Manual

Details

biocViews	Classification, Clustering, DimensionReduction, FeatureExtraction, GenePrediction, ImmunoOncology, Metabolomics, Metagenomics, Microarray, MultipleComparison, Proteomics, Regression, Sequencing, Software, TimeCourse
Version	1.11.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-3
Depends	mixOmics, R (>= 4.0)
Imports	dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest, plyr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots
SystemRequirements
Enhances
URL
BugReports	https://github.com/abodein/timeOmics/issues
Depends On Me
Imports Me
Suggests Me	netOmics
Links To Me
Build Report

Package Archives

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

Source Package	timeOmics_1.11.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/timeOmics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/timeOmics
Package Short Url	https://bioconductor.org/packages/timeOmics/
Package Downloads Report	Download Stats