From 5a13922697d4d240dea4d16140b0eb749203e713 Mon Sep 17 00:00:00 2001 From: Dimitrios Vitsios Date: Wed, 20 Nov 2019 14:33:34 +0000 Subject: [PATCH] Update README.md --- README.md | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 154ce8d..269051a 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,9 @@ - [Introduction](#introduction) - [Installation](#installation) - [Run](#run) + - [mantisml](#mantisml) + - [mantisml-profiler](#mantisml-profiler) + - [mantisml-overlap](#mantisml-overlap) @@ -114,7 +117,8 @@ Other example config files can be found under [example-input](example-input) or -## `mantisml` +`mantisml` +========= You need to provide a config file (`.yaml`) and an output directory.
You may also define the number of threads to use (`-n` option; default value: 4). @@ -138,7 +142,8 @@ Output figures from all steps during the `mantis-ml` run (e.g. *Exploratory Data
-## `mantisml-profiler` +`mantisml-profiler` +================== #### Preview selected phenotypes and features (optional) You may preview all selected phenotypes and relevant features based on your input config file parameters by running the `mantisml-profiler` command. @@ -151,7 +156,9 @@ mantisml-profiler [-v] -c [config_file] -o [output_dir]

-## `mantisml-overlap` +`mantisml-overlap` +================== + #### Run enrichment test between mantis-ml predictions and an external ranked gene list to get refined gene predictions To run `mantisml-overlap`, you need to provide a config file (`.yaml`), an output directory with `mantisml` results and an external ranked gene list file (`mantisml` has to be run already given the same ouput directory).