Add sections installation, usage and funding

README.md

@@ -1,13 +1,41 @@
-# IDR2D
+# IDR2D: Irreproducible Discovery Rate for Genomic Interactions
 
 [![license: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://opensource.org/licenses/MIT) [![Travis build status](https://travis-ci.org/kkrismer/idr2d.svg?branch=master)](https://travis-ci.org/kkrismer/idr2d) [![DOI](https://img.shields.io/badge/DOI-10.1101%2F691295-blue.svg)](https://doi.org/10.1101/691295) [![BioC](https://img.shields.io/badge/BioC-0.99.7-brightgreen.svg)](https://doi.org/doi:10.18129/B9.bioc.idr2d) [![platforms](https://bioconductor.org/shields/availability/3.10/idr2d.svg)](https://bioconductor.org/packages/devel/bioc/html/idr2d.html#archives)
 
 Chromatin interaction data from protocols such as ChIA-PET and HiChIP provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce a generalization of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments.
 
+## Installation
+
+The *idr2d* package is currently part of the development branch of Bioconductor and will be available on the release branch once Bioconductor 3.10 replaces Bioconductor 3.9. This transition is scheduled for October 30 2019.
+
+In the meantime, *idr2d* can be installed from the development branch:
+
+```
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+# The following initializes usage of Bioc devel
+BiocManager::install(version='devel')
+
+BiocManager::install("idr2d")
+```
+
+R 3.6 (or higher) is required. Additionally, the 64-bit version of Python 3.5 (or higher) and the Python package [hic-straw](https://pypi.org/project/hic-straw/) are required for HiC analysis from *.hic* files. 
+
+## Usage
+
+There are two vignettes available on Bioconductor, focusing on [*idr2d* and ChIA-PET data](https://bioc.ism.ac.jp/packages/devel/bioc/vignettes/idr2d/inst/doc/idr2d.html) and [*idr2d* and ChIP-seq data](https://bioc.ism.ac.jp/packages/devel/bioc/vignettes/idr2d/inst/doc/idr1d.html).
+
+The [reference manual](https://bioc.ism.ac.jp/packages/devel/bioc/manuals/idr2d/man/idr2d.pdf) might also be helpful if you know what you are looking for.
+
 ## Citation
 
 If you use IDR2D in your research, please cite:
 
 **IDR2D identifies reproducible genomic interactions**  
 Konstantin Krismer, Yuchun Guo, and David K. Gifford
 bioRxiv 691295; DOI: https://doi.org/10.1101/691295
+
+## Funding
+
+The development of this method was supported by National Institutes of Health (NIH) grants 1R01HG008363 and 1R01NS078097, and the MIT Presidential Fellowship.