diff --git a/README.md b/README.md index 50a51e9c..607e713b 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,41 @@ DANCE is a Python toolkit to support deep learning models for analyzing single-c Our goal is to build up a deep learning community for single cell analysis and provide GNN based architecture for users for further development in single cell analysis. +## Usage + +### Overview + +In release 1.0, the main usage of the PyDANCE is to provide readily available experiment reproduction +(see detail information about the reproduced performance [below](#implemented-algorithms)). +Users can easily reproduce selected experiments presented in the original papers for the computational single-cell methods implemented in PyDANCE, which can be found under [`examples/`](examples). + +### Motivation + +Computational methods for single-cell analysis are quickly emerging, and the field is revolutionizing the usage of single-cell data to gain biological insights. +A key challenge to continually developing computational single-cell methods that achieve new state-of-the-art performance is reproducing previous benchmarks. +More specifically, different studies prepare their datasets and perform evaluation differently, +and not to mention the compatibility of different methods, as they could be written in different languages or using incompatible library versions. + +PyDANCE addresses these challenges by providing a unified Python packge implementing many popular computational single-cell methods (see [Implemented Algorithms](#implemented-algorithms)), +as well as easily reproducible experiments by providing unified tools for + +- Data downloading +- Data (pre-)processing and transformation (e.g. graph construction) +- Model training and evaluation + +### Example: runing cell-type annotation benchmark using scDeepSort + +- Step0. Install PyDANCE (see [Installation](#installation)) +- Step1. Navigate to the folder containing the corresponding example scrtip. + In this case, it is [`examples/single_modality/cell_type_annotation`](examples/single_modality/cell_type_annotation). +- Step2. Obtain command line interface (CLI) options for a particular experiment to reproduce at the end of the + [script](examples/single_modality/cell_type_annotation/scdeepsort.py). + For example, the CLI options for reproducing the `Mouse Brain` experiment is + ```bash + python scdeepsort.py --data_type scdeepsort --tissue Brain --test_data 2695 + ``` +- Step3. Wait for the experiment to finsh and check results. + ## Installation