Update doc, test and README

README.md

@@ -1,3 +1,66 @@
 # Cell BLAST
 
-An accurate and robust solution to large-scale cell querying
+Cell BLAST is a cell querying tool for single-cell transcriptomics data.
+
+For each query cell, it searches for most similar cells in the reference database.
+Annotations in reference cells, e.g. cell type, can then be transfered to query
+cells based on cell-to-cell similarities. See our
+[preprint](https://www.biorxiv.org/content/10.1101/587360v1) for details.
+
+![flowchart](doc/_static/flowchart.png)
+
+## Installing the python package
+
+We only support installation via pip right now.
+
+Installation within virtual environments are recommended, see
+[virtualenv](https://virtualenv.pypa.io/en/latest/) or
+[conda](https://conda.io/docs/user-guide/tasks/manage-environments.html).
+
+For conda, here's a one-liner to set up an empty environment
+for installing Cell BLAST:
+
+`conda create -n cb python=3.6 && source activate cb`
+
+Now follow the instructions below to install Cell BLAST:
+
+1. Make sure you have a working version of tensorflow or tensorflow-gpu
+   (version >= 1.5). You can follow the
+   [official instructions](https://www.tensorflow.org/install/)
+   about how to install tensorflow (and dependencies like CUDA and CuDNN
+   for the GPU version), or just install via anaconda, which handles
+   dependencies automatically:
+
+   For installing the GPU supported version:
+   `conda install tensorflow-gpu=1.8`
+
+   For installing the CPU only version:
+   `conda install tensorflow=1.8`
+
+2. Install Cell BLAST by running:
+   `pip install Cell-BLAST`
+
+3. Check if the package can be imported in python interpreter:
+   `import Cell_BLAST as cb`
+
+Online documentation can be found [here](http://cblast.gao-lab.org/doc/index.html).
+
+## Web-based interface
+
+We also provide a [Web-based service](http://cblast.gao-lab.org/) for
+off-the-shelf querying of our ACA reference panels.
+
+## Repository structure
+
+* The `Cell_BLAST` directory contains the Cell BLAST python package.
+* The `Datasets` directory contains scripts used for building the ACA database.
+* The `Evaluation` directory contains scripts used for benchmarking
+  and producing some figures of the manuscript.
+* The `doc` directory contains files used to generate the online documentation.
+* The `test` directory contains unit tests for the python package.
+
+## Contact
+
+Feel free to submit an issue or contact us at
+[[email protected]](mailto:[email protected])
+for problems about the python package, website or database.

doc/index.rst

@@ -7,18 +7,14 @@ Welcome to Cell BLAST's documentation!
 ======================================
 
 **Cell_BLAST** is a single cell transcriptome querying tool, based on
-a deep learning model, **DIRECTi**, which supports:
+a deep generative model (currently named **DIRECTi**).
 
-* Learning low dimensional cell embedding with intrinsic data clustering
-* Semi-supervision
-* Removal of batch effect / systematical bias
-
-**Cell_BLAST** then performs query based on parametric cell embeddings from
-**DIRECTi**, using posterior distribution distances.
-
-Information like cell type annotation can then be transferred from reference
-to query data based on Cell BLAST hits.
+**Cell_BLAST** performs querying based on parametric cell embeddings from
+**DIRECTi**, using posterior distribution distances. Information like cell type
+annotation can then be transferred from reference to query data based on
+Cell BLAST hits.
 
+.. image:: _static/flowchart.png
 
 Contents
 ========

doc/install.rst

@@ -3,35 +3,36 @@
 Installation Guide
 ==================
 
-We only support installation with local archive right now.
+We only support installation via pip right now.
 
 Installation within virtual environments are recommended, see
 https://virtualenv.pypa.io/en/latest/ or
 https://conda.io/docs/user-guide/tasks/manage-environments.html.
 
 For conda, here's a one-liner to set up an empty environment
-for ``Cell_BLAST``:
+for installing Cell BLAST:
 
-``conda create -n cb -c anaconda python=3.6 && source activate cb``
+``conda create -n cb python=3.6 && source activate cb``
 
-Now follow the instructions below to install ``Cell_BLAST``:
+Now follow the instructions below to install Cell BLAST:
 
 1. Make sure you have a working version of tensorflow or tensorflow-gpu
    (version >= 1.5). You can follow the instructions on
    https://www.tensorflow.org/install/ about how to install tensorflow
    (and dependencies like CUDA and CuDNN for the GPU version), or just install
-   via the conda, which handles dependencies automatically:
+   via anaconda, which handles dependencies automatically:
 
    For installing the GPU supported version:
-   ``conda install -c anaconda tensorflow-gpu=1.8``
+   ``conda install tensorflow-gpu=1.8``
 
    For installing the CPU only version:
-   ``conda install -c anaconda tensorflow=1.8``
+   ``conda install tensorflow=1.8``
 
-2. Download latest Cell_BLAST release from:
-   https://github.com/gao-lab/Cell_BLAST/releases/.
+2. Install Cell BLAST by running:
+   ``pip install Cell-BLAST``.
 
-3. Install by ``pip install Cell_BLAST-<version>.tar.gz``
+3. Check if the package can be imported in python interpreter:
+   ``import Cell_BLAST as cb``
 
 And you are good to go.
 

test/.gitignore

@@ -0,0 +1 @@
+!pollen.h5