timeOmics
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see timeOmics.
Time-Course Multi-Omics data integration
Bioconductor version: 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("timeOmics")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
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) (4 years) |
| License | GPL-3 |
| Depends | mixOmics, lmms, R (>= 4.0) |
| Imports | dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest |
| 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 | |
| Links To Me | |
| Build Report | 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 |
| 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 3.11 | Source Archive |