Commit 9c5e5977 authored by Aurelien Brionne's avatar Aurelien Brionne
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readme

parent 7ad710a3
...@@ -4,7 +4,7 @@ Title: Multiple genomic features annotations ...@@ -4,7 +4,7 @@ Title: Multiple genomic features annotations
Authors@R: c( Authors@R: c(
person("Aurelien","Brionne", role=c("aut","cre"), person("Aurelien","Brionne", role=c("aut","cre"),
email="aurelien.brionne@inra.fr")) email="aurelien.brionne@inra.fr"))
Depends: R (>= 3.1.0) Depends: R (>= 3.5.1)
Imports: Imports:
AnnotationDbi, AnnotationDbi,
data.table, data.table,
...@@ -21,7 +21,7 @@ Suggests: ...@@ -21,7 +21,7 @@ Suggests:
githubinstall githubinstall
Description: The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority. Description: The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
VignetteBuilder: knitr VignetteBuilder: knitr
License: MIT License: GPL-3
LazyData: TRUE LazyData: TRUE
Author: Aurelien Brionne [aut, cre] Author: Aurelien Brionne [aut, cre]
Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr> Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
......
YEAR: 2018
COPYRIGHT HOLDER: Institut National de la Recherche Agronomique (INRA)
# 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. 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"/>
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5. Get annotation table: `GenomeFeatures::Table`.
<img src="./inst/extdata/table.png" align="left"/>
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6. Features ovelaps.
<img src="./inst/extdata/data/output/upset_H3K4Me3_J35.png" align="left"/>
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