timeOmics

DOI: 10.18129/B9.bioc.timeOmics  

Time-Course Multi-Omics data integration

Bioconductor version: Release (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")

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
Text		NEWS

Details

biocViews	Classification, Clustering, DimensionReduction, FeatureExtraction, GenePrediction, ImmunoOncology, Metabolomics, Metagenomics, Microarray, MultipleComparison, Proteomics, Regression, Sequencing, Software, TimeCourse
Version	1.12.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	GPL-3
Depends	mixOmics, R (>= 4.0)
Imports	dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, 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_1.12.0.tar.gz
Windows Binary	timeOmics_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	timeOmics_1.12.0.tgz
macOS Binary (arm64)	timeOmics_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/timeOmics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/timeOmics
Bioc Package Browser	https://code.bioconductor.org/browse/timeOmics/
Package Short Url	https://bioconductor.org/packages/timeOmics/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive