From a84a23eb5cd0be0e0790264be13c91c0dedd4d21 Mon Sep 17 00:00:00 2001
From: Mark Cheng <89597443+TKMarkCheng@users.noreply.github.com>
Date: Mon, 10 Feb 2025 00:54:45 +0000
Subject: [PATCH] Update README.md for conda users

Adding some lines to help future fellow conda/mamba users who would may run into issues when R is not locally installed or if the local R is not preferred.
---
 README.md | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/README.md b/README.md
index f369f82..2a4d695 100644
--- a/README.md
+++ b/README.md
@@ -19,6 +19,14 @@ git clone https://github.com/emdann/milopy.git
 cd milopy
 pip install .
 ```
+for conda users who have trouble installing with `pip install .` (An R instance needs to co-exist in the same environment).
+```bash
+conda install conda-forge::r-base
+git clone https://github.com/emdann/milopy.git
+cd milopy
+pip install .
+```
+
 
 ## Tutorial
 
@@ -31,6 +39,18 @@ pip install .
 import scanpy as sc
 import numpy as np
 
+import milopy
+import milopy.core as milo
+```
+for conda users (The R root needs to be explicitly called to the running .ipynb session).
+```python
+import scanpy as sc
+import numpy as np
+
+import os
+import sys
+os.environ['R_HOME'] = sys.prefix + "\\lib\\R"
+
 import milopy
 import milopy.core as milo
 ```