timeOmics

DOI: 10.18129/B9.bioc.timeOmics    

Time-Course Multi-Omics data integration

Bioconductor version: Release (3.11)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.1
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License GPL-3
Depends mixOmics, lmms, R (>= 4.0)
Imports dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest
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
Links To Me
Build Report  

Package Archives

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

Source Package timeOmics_1.0.1.tar.gz
Windows Binary timeOmics_1.0.1.zip
macOS 10.13 (High Sierra) timeOmics_1.0.1.tgz
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
Old Source Packages for BioC 3.11 Source Archive

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