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timeOmics

Time-Course Multi-Omics data integration


Bioconductor version: Release (3.18)

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>

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

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")
timeOmics HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, DimensionReduction, FeatureExtraction, GenePrediction, ImmunoOncology, Metabolomics, Metagenomics, Microarray, MultipleComparison, Proteomics, Regression, Sequencing, Software, TimeCourse
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends mixOmics, R (>= 4.0)
Imports dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr
System Requirements
URL
Bug Reports https://github.com/abodein/timeOmics/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me netOmics
Links To Me
Build Report Build Report

Package Archives

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

Source Package timeOmics_1.14.0.tar.gz
Windows Binary timeOmics_1.14.0.zip (64-bit only)
macOS Binary (x86_64) timeOmics_1.14.0.tgz
macOS Binary (arm64) timeOmics_1.14.0.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