This is the repository of the R package sigident.func. It provides functional analysis and is part of the sigident package framework: https://github.com/miracum/clearly-sigident
The functional analysis includes the following steps:
- DEG analysis
- Gene enrichment
- Test for over-representation
- GO enrichment analysis
You can install sigident.func with the following commands in R:
install.packages("devtools")
devtools::install_github("miracum/clearly-sigident.func")Please study the package's vignette for a detailed example.
Since the building the package vignette takes rather long (~ 20 min.), we provide the already built vignettes in this repository.
The sigident.func package is under active development and not on CRAN yet - this means, that from time to time, the API can break, due to extending and modifying its functionality. It can also happen, that previoulsy included functions and/or function arguments are no longer supported. However, a detailed package vignette will be provided alongside with every major change in order to describe the currently supported workflow.
- about CLEARLY: https://www.transcanfp7.eu/index.php/abstract/clearly.html
- about MIRACUM: https://www.miracum.org/
- about the Medical Informatics Initiative: https://www.medizininformatik-initiative.de/index.php/de