diff --git a/README.md b/README.md index 93aad8f..1d257fd 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,28 @@ As an output, a networkx graph of the gene regulatory network with integrated sc +## System requirements + +### Hardware requirements + +`snp2cell` can run on a standard computer with enough RAM to hold the used datasets in memory. +It can make use of multiple CPUs to speed up computations. + +### Software requirements + +**OS requirements** + +The package has been tested on: + +- macOS Monterey (12.6.7) +- Linux: Ubuntu 22.04 jammy + +**Python requirements** + +A python version `>=3.5` and `<3.12` is required for all dependencies to work. +Various python libraries are used, listed in `setup.py`, including the python scientific stack, `networkx` and `scanpy`. +`snp2cell` and all dependencies can be installed via `pip` (see below). + ## Installation *Optional: create and activate a new conda environment (with python<3.12):* @@ -20,16 +42,33 @@ mamba create -n snp2cell "python<3.12" mamba activate snp2cell ``` -Install snp2cell: +### Install with pip + +**from PyPI** + +*will be added* + +**from github** + ```bash pip install git+ssh://git@github.com/JPatrickPett/snp2cell.git ``` +*(installation time: around 2 min)* + ## Usage +**Python module** + snp2cell can be imported as a python module (see [notebooks](#example-notebooks) for examples). -Additionally, there is also a command line interface: +Demo: A minimal demo can be found [here](https://github.com/Teichlab/snp2cell/blob/main/docs/source/toy_example.ipynb) as a jupyter notebook and as a unit test in `test/test_toy_example.py`. (*running time: around 12 sec*) + +**CLI** + +Importing `snp2cell` as a python module gives most flexibility. +Additionally, there is a command line interface. To see all options, run: + ```bash snp2cell --help ```