updated install instructions

README.md

@@ -4,7 +4,7 @@
 
 ## sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data.
 
-[![DOI](https://zenodo.org/badge/271841139.svg)](https://zenodo.org/badge/latestdoi/271841139) [![Documentation Status](https://readthedocs.org/projects/sincei/badge/?version=latest)](https://sincei.readthedocs.io/en/latest/?badge=latest) [![PyPI Version](https://img.shields.io/pypi/v/sincei.svg?style=plastic)](https://pypi.org/project/sincei/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![test](https://github.com/vivekbhr/sincei/actions/workflows/test.yml/badge.svg)](https://github.com/vivekbhr/sincei/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/vivekbhr/sincei/graph/badge.svg?token=VRTMITHHBI)](https://codecov.io/gh/vivekbhr/sincei)
+[![DOI](https://zenodo.org/badge/271841139.svg)](https://zenodo.org/badge/latestdoi/271841139) [![Documentation Status](https://readthedocs.org/projects/sincei/badge/?version=latest)](https://sincei.readthedocs.io/en/latest/?badge=latest) [![PyPI Version](https://img.shields.io/pypi/v/sincei.svg?style=plastic)](https://pypi.org/project/sincei/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![test](https://github.com/vivekbhr/sincei/actions/workflows/test.yml/badge.svg)](https://github.com/vivekbhr/sincei/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/vivekbhr/sincei/graph/badge.svg?token=VRTMITHHBI)](https://codecov.io/gh/vivekbhr/sincei) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sincei/README.html)
 
 ## Features
 
@@ -23,18 +23,18 @@ Please browse the full documentation for tutorials on how to use sincei on comma
 
 sincei is a command line toolkit based on python3, and can be installed using [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
 
-Create a new conda environment and install sincei stable release from github using:
+The recommended way to install sincei is via bioconda:
 
 ```
-conda create -n sincei -c anaconda python=3.8
-conda activate sincei
-(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@master#egg=sincei
+conda create -n sincei -c bioconda -c conda-forge sincei
 ```
 
-For the development version, try:
+Alternatively, a development version can be installed via GitHub.
 
 ```
-(sincei): pip install --editable=git+https://github.com/vivekbhr/sincei.git@develop#egg=sincei
+conda create -n sincei -c anaconda python=3.8
+conda activate sincei
+(sincei): pip install --editable=git+https://github.com/bhardwaj-lab/sincei.git@master#egg=sincei
 ```
 
 ## Usage

docs/index.rst

@@ -16,31 +16,61 @@
     :target: https://pypi.org/project/sincei/
     :alt: PyPI Version
 
+.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
+    :target: http://bioconda.github.io/recipes/sincei/README.html
+    :alt: Install with bioconda
+
 Bhardwaj V. and Mourragui S. (2023) sincei: A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data.
 
 
+=================
+Installation
+=================
 
+sincei is a command line toolkit based on python3. The stable version of sincei can be installed using `conda <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_ , while the development versions can be installed from github via pip.
 
-Installation
--------------------
-sincei is a command line toolkit based on python3, and can be installed using `conda <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_
+Installation via bioconda
+---------------------------
+
+Create a new conda environment and install sincei in it using:
+
+.. code-block:: bash
+
+    conda create -n sincei -c bioconda -c conda-forge sincei
+
+Users of Mac with Arm architecture (M1-3 macbooks and beyond) should explicitly specify the osx-64 version to allow dependencies to install properly.
+
+.. code-block:: bash
+
+    conda create -n sincei --subdir 'osx-64' -c bioconda -c conda-forge sincei
 
-Create a new conda environment and install sincei using:
+*Note:* The dependency `mctorch-lib` required for `scClusterCells` is currently unavailable via conda, therefore, to use `scClusterCells`, we recommend installing it separately via pip.
+
+.. code-block:: bash
+
+    # install mctorch-lib
+    (sincei): pip install mctorch-lib
+    (sincei): scClusterCells --help
+
+
+Installation via github
+---------------------------
+
+Create a new conda environment and install sincei in it using pip from GitHub:
 
 .. code-block:: bash
 
     conda create -n sincei -c anaconda python=3.8
     conda activate sincei
-    (sincei): pip install git+https://github.com/vivekbhr/sincei.git@master#egg=sincei
+    (sincei): pip install git+https://github.com/bhardwaj-lab/sincei.git@master#egg=sincei
 
 
 Getting Help
 ------------
 
-* For all kind of questions, suggesting changes/enhancements or to report bugs, please create an issue on `our GitHub repository <https://github.com/vivekbhr/sincei>`_
-
-**Please Note that sincei is under active development.** Some features might be incomplete, untested or might be removed as we move towards a stable version.
+* For questions related to usage, or suggesting changes/enhancements please use our `GitHub discussion board <https://github.com/bhardwaj-lab/sincei/discussions>`__ . To report bugs, please create an issue on `our GitHub repository <https://github.com/bhardwaj-lab/sincei>`_
 
+**Please Note that sincei is under active development.** We expect significant changes/updates as we move towards our first major release (1.0).
 
 
 The list of tools available in sincei