From c992b3ef08c7c9dfd4ccf1cb27722d32acbc3e7d Mon Sep 17 00:00:00 2001
From: Sebastian Gregoricchio
 <52447016+sebastian-gregoricchio@users.noreply.github.com>
Date: Tue, 5 Jan 2021 12:06:59 +0100
Subject: [PATCH] Update index.md

---
 index.md | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/index.md b/index.md
index c4e4cee..13a2674 100644
--- a/index.md
+++ b/index.md
@@ -14,21 +14,20 @@ To install them directly you need to have previously installed `BiocManager` and
 BiocManager::install(c("Biostrings", "biomaRt", "GO.db", "rtracklayer"))
 ```
 
-### DeepTools
+### deepTools
 Certain functions of this package require that `deeptools` is installed on your system. For more information see the [deepTools](https://deeptools.readthedocs.io/en/develop/content/installation.html) installation page.
-
-#### Installation via `conda`
-```bash
-conda install -c bioconda deeptools
-```
-
-#### Command line installation using `pip`
-Install deepTools using the following command:
-```python
-pip install deeptools
-```
-All python requirements should be automatically installed.
-
+* **Installation via `conda`**: `conda install -c bioconda deeptools`
+* **Command line installation using `pip`**: `pip install deeptools`, All python requirements should be automatically installed.
+
+
+### bedTools
+Certain functions of this package require that `bedtools` is installed on your system. For more information see the [bedTools](https://bedtools.readthedocs.io/en/latest/content/installation.html) installation page.
+* **Installation via `conda`**: `conda install -c bioconda bedtools`
+* **Command line installation**:
+    - Fedora/Centos: `yum install BEDTools`
+    - Debian/Ubuntu: `apt-get install bedtools`
+    - Homebrew (MacOS): `brew tap homebrew/science; brew install bedtools`
+    - MacPorts: `port install bedtools`
 
 
 ## Installation