timeOmics
This is the released version of timeOmics; for the devel version, see timeOmics.
Time-Course Multi-Omics data integration
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 |
| Depends | mixOmics, R (>= 4.0) |
| Imports | dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate |
| 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | timeOmics_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | timeOmics_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | timeOmics_1.24.0.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 |