document extra dependencies

docs/install.md

@@ -69,11 +69,16 @@ pip install .
 Optional dependencies
 ---------------------
 
-Here is a list of optional dependencies used by SnapATAC2:
+`pip install snapatac2` installs the essential dependencies needed for SnapATAC2.
+For certain features, however, additional optional dependencies are necessary:
 
-- `macs2`: Peak calling.
-- `harmonypy`: Batch correction using the Harmony.
-- `xgboost`: Regulatory network analysis.
+- harmonypy: For the `snapatac2.pp.harmony` function.
+- scanorama: For the `snapatac2.pp.scanorama_integrate` function.
+- xgboot: For network structure inference.
 
-Optional dependencies are not installed by SnapATAC2. Please install them
-manually if necessary.
+To install these optional dependencies, use `pip install snapatac2[extra]`.
+
+For downstream analysis, some helpful but not mandatory packages, such as scanpy and scvi-tools, are available.
+They can be installed with `pip install snapatac2[recommend]`.
+
+To obtain all optional dependencies at once, use `pip install snapatac2[all]`.

snapatac2-python/setup.py

@@ -36,6 +36,7 @@
         "anndata>=0.8.0",
         "kaleido",
         "multiprocess",
+        "MACS2>=2.2.7",
         "natsort",
         "numpy>=1.16.0",
         "pandas",
@@ -53,4 +54,9 @@
         "typing_extensions",
         "umap-learn>=0.5.0",
     ],
+    extras_require={
+        'extra': ['scanorama>=1.7.3', 'harmonypy>=0.0.9', 'xgboost>=1.4'],
+        'recommend': ['scanpy>=1.9', 'scvi-tools>=1.0'],
+        'all': ['snapatac2[extra]', 'snapatac2[recommend]']
+    }
 )