From 399129346c1dd3953936c145af57bbe22582c33b Mon Sep 17 00:00:00 2001
From: Kaitlin Sullian <54858629+kaitsull@users.noreply.github.com>
Date: Sun, 12 Dec 2021 15:10:48 -0800
Subject: [PATCH] update instructions

---
 README.md | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 68a496f..845586e 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,14 @@
-# proteinsearch
-An automated web search for human antibodies labelling neurons and glia in the brain. Takes the direct output of Seurat's "FindMarkers()" and returns a data frame of antibodies based on information from the human protein atlas.
+# proteinsearch.py  
+An automated web search for human antibodies labelling neurons and glia in the brain.   
+This code takes the direct output of Seurat's `FindMarkers()` and returns a data frame of antibodies based on information from the human protein atlas.  
+
+
+## Instructions:  
+1. Save a `.csv` of the marker genes for your single cell RNA sequencing data: `write.csv(FindMarkers(data), markers.csv)`
+2. In your terminal, ensure that Selenium web driver is installed: `pip install selenium`
+3. Download Chrome driver [here](https://chromedriver.chromium.org/downloads).
+4. In the terminal, navigate to the directory holding `proteinsearch.py`.
+5. In the terminal, type: `python proteinsearch.py`
+6. Enter the absolute path of your marker gene csv.
+7. Enter the name of of the output file (be sure to include .csv at the end).
+8. Chrome driver will open and begin the search!