https://github.com/bioconductor-source/timeomics
Science Score: 26.0%
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Low similarity (13.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Size: 3.6 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
timeOmics
timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data (A.) 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:
- a pre-processing step (B.) Normalize and filter low-expressed features, except those not varying over time,
- a modelling step (C.) Capture inter-individual variability in biological/technical replicates and accommodate heterogeneous experimental designs,
- a clustering step (D.) Group features with the same expression profile over time. Feature selection step can also be used to identify a signature per cluster,
- a post-hoc validation step (E.) Ensure clustering quality.
timeOmics can be applied on both single-Omic or multi-Omics experimental design.
If you came to this page thanks to our article and you wish to access its example scripts please follow this link .
Installation
Latest GitHub Version
Install the devtools package in R, then load it and install the latest stable version of timeOmics from GitHub
```r
install devtools if not installed
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
install timeOmics
devtools::install_github("abodein/timeOmics") ```
Citing
Bodein A, Chapleur O, Droit A and Lê Cao K-A (2019) A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types. Front. Genet. 10:963. doi:10.3389/fgene.2019.00963
Maintainer
Antoine Bodein (antoine.bodein.1@ulaval.ca)
Bugs/Feature requests
If you have any bugs or feature requests, let us know. Thanks!
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
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Dependencies
- R >= 4.0 depends
- mixOmics * depends
- checkmate * imports
- dplyr * imports
- ggplot2 * imports
- ggrepel * imports
- lmtest * imports
- magrittr * imports
- plyr * imports
- purrr * imports
- stringr * imports
- tibble * imports
- tidyr * imports
- BiocStyle * suggests
- gplots * suggests
- igraph * suggests
- knitr * suggests
- rmarkdown * suggests
- snow * suggests
- testthat * suggests
- tidyverse * suggests