README.md
In CompEpigen/FactorViz: Visualization app for methylome decomposition experiments

FactorViz 2.0

FactorViz provides an interactive visualization and reporting environment for exploring the results of the methylome decomposition experiments carried out by MeDeCom or similar deconvolution tools. It is the interpretation tool used in a recently published protocol to perform reference free deconvolution of complex DNA methylation data.

Installation

You can install the FactorViz through GitHub using devtools:

{r, eval=F} install.packages("devtools") devtools::install_github("CompEpigen/FactorViz")

Installation has been tested on the following operating systems:

Type | Distribution | Version | R-version | Installation successful | Protocol tested | Comments ---- | ---- | ---- | ---- | ---- | ---- | ---- Linux | Debian | Wheezy (7) | R-3.5.2 | Yes | Yes | Linux | Debian | Wheezy (7) | R-3.6.0 | Yes | Yes | Linux | Debian | Jessie (8) | R-3.5.3 | Yes | Yes (reduced) | Linux | Debian | Jessie (8) | R-3.6.1 | Yes | No | Linux | Debian | Jessie (8) | R-4.0 | Yes | No | Linux | Debian | Buster (10) | R-3.5.2 | Yes | Yes (reduced) | Linux | Fedora | 28 | R-3.5.3 | Yes | No | Linux | Fedora | 31 | R-3.6.1 | No | Yes (reduced) | `igraph' dependency fails to install Linux | CentOS | 8.0 | R-3.5.2 | Yes | Yes (reduced) | Linux | CentOS | 8.0 | R-3.6.1 | Yes | Yes (reduced) | Linux | Ubuntu | 19 | R-3.6.1 | Yes | Yes (reduced) | MacOS | | Mojave | R-3.5.1 | Yes | Yes (reduced) | binary release used MacOS | | Catalina | R-3.6.0 | Yes | Yes (reduced) | Windows | 10 | Pro | R-3.6.1 | No | Yes (reduced) | Use docker image https://hub.docker.com/r/mscherer/medecom Windows | 7 | Pro | R-3.6.1 | No | No | Docker is not available for Windows 7

Using FactorViz

You can start FactorViz by using startFactorViz() command, and then specify the output from DecompPipeline. A more detailed introduction into FactorViz can be found in the package vignette.