timeOmics

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see timeOmics.

Time-Course Multi-Omics data integration

Bioconductor version: 3.13

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, DimensionReduction, FeatureExtraction, GenePrediction, ImmunoOncology, Metabolomics, Metagenomics, Microarray, MultipleComparison, Proteomics, Regression, Sequencing, Software, TimeCourse

Version 1.4.0

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, propr, lmtest, plyr

System Requirements

URL

Bug Reports https://github.com/abodein/timeOmics/issues

Suggests BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots

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 timeOmics_1.4.0.tar.gz

Windows Binary timeOmics_1.4.0.zip

macOS 10.13 (High Sierra) timeOmics_1.4.0.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 3.13 Source Archive