readme

DESCRIPTION

@@ -4,7 +4,7 @@ Title: Multiple genomic features annotations
 Authors@R: c(
 	person("Aurelien","Brionne", role=c("aut","cre"),
 	email="aurelien.brionne@inra.fr"))
-Depends: R (>= 3.1.0)
+Depends: R (>= 3.5.1)
 Imports:
     AnnotationDbi,
     data.table,
@@ -21,7 +21,7 @@ Suggests:
    githubinstall
 Description: The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
 VignetteBuilder: knitr
-License: MIT
+License: GPL-3
 LazyData: TRUE
 Author: Aurelien Brionne [aut, cre]
 Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>

LICENSE

-YEAR: 2018
-COPYRIGHT HOLDER: Institut National de la Recherche Agronomique (INRA)

README.md

-# GenomeFeatures
+<img src="./inst/extdata/univ.png" align="right"/>
+<img src="./inst/extdata/boa.png" align="right"/>
+<img src="./inst/extdata/inra.png" align="right"/>
 
-## Aim
+# GenomeFeatures R package
 
 The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
 
-## vignette style package
+## Installation
 
-source("https://bioconductor.org/biocLite.R")
+`devtools::install_github("abrionne/GenomeFeatures", build_vignettes=TRUE)`
 
-biocLite("BiocStyle")
+## Quick overview
 
-## GenomeFeatures Install
+1. load peaks file: `GenomeFeatures::readPeakFile`.
 
-devtools::install_github("abrionne/GenomeFeatures", build_vignettes=TRUE)
+2. Build a convenient object for find overlaps beetween all selected features and genomic coordinates targets: `GenomeFeatures::build_genome_features`.
+
+3. Find overlaps beetween genomic coordinates and features: `GenomeFeatures::genome_features_overlaps`.
+
+4. Features plot: `GenomeFeatures::Plot`.
+
+<img src="./inst/extdata/barplot.png" align="left"/>
+
+<img src="./inst/extdata/lineplot.png" align="left"/>
+
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+
+5. Get annotation table: `GenomeFeatures::Table`.
+
+<img src="./inst/extdata/table.png" align="left"/>
+
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+</br>
+
+6. Features ovelaps.
+
+<img src="./inst/extdata/data/output/upset_H3K4Me3_J35.png" align="left"/>