From 99fa8335de08caf60ec48efbe8a1a89cea90c118 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dar=C3=ADo=20Here=C3=B1=C3=BA?= Date: Mon, 15 Jun 2020 12:22:40 -0300 Subject: [PATCH] Minor formatting proposals --- README.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index b7bb3b6..aee95ae 100644 --- a/README.md +++ b/README.md @@ -1,20 +1,20 @@ -MethICA -======== +# MethICA Methylation signature analysis with independent component analysis. Description: apply independent component analysis (ICA) to methylation data to extract epigenetic signatures and perform downstream analyses and representations to interpret the biological meaning of methylation components. ## Installation -======== -Install from the GitHub repository using devtools: +Install from the GitHub repository using devtools: +``` install.packages("devtools") library(devtools) devtools::install_github("FunGeST/MethICA") +``` ## Input files -======== + For the extraction of methylation signature _MethICA_ requires one mandatory input file -- a **methylation level** file (bval) describing methylation levels of individual CpG sites or genomic regions (row) in each sample (column). Two additional files are needed for the interpretation of methylation components: a **CpG annotation** file describing the epigenetic context of CpG sites, and a **sample annotation** providing any relevant information about the samples. **The input files should have the following format. Example input files are provided with the package.** @@ -46,14 +46,13 @@ For the extraction of methylation signature _MethICA_ requires one mandatory inp * `Sample`: Sample identifier. Any alphanumeric string. ## Running MethICA -================ * The [RUNNING\_METHICA\_EXAMPLE](https://github.com/FunGeST/MethICA) folder contains an example dataset and an R script of a typical MethICA analysis. Please try!
* [*Introduction to MethICA*] provides a comprehensive example of the MethICA workflow with detailed explanations of each function.
## License -======== + Copyright (C) 2020 Léa Meunier