Metadata-Version: 2.1
Name: capital
Version: 1.0.0
Summary: Single-Cell Analysis, comparing pseudotime trajectories                 with tree alignment
Home-page: https://github.com/ykat0/capital
Author: Reiichi Sugihara, Yuki Kato, Tomoya Mori, Yukio Kawahara
Author-email: reiichi.sugihara@gmail.com
License: BSD-3-Clause
Description: # CAPITAL
        
        ### Comparative pseudotime analysis of single-cell RNA-seq data
        
        Last updated: 2021-01-12
        
        We present CAPITAL, a computational method for comparing pseudotime trajectories with tree alignment whereby trajectories including branchings can be automatically compared.
        
        ## Installation
        * CAPITAL (ver. 1.0.0) in Python
        
        ### Requirements
        * Python>=3.8 ([Miniconda](https://docs.conda.io/en/latest/miniconda.html) is recommended)
        * anndata>=0.7.4
        * graphtools
        * graphviz
        * h5py<=2.10
        * leidenalg
        * magic-impute
        * matplotlib>=3.1.2
        * networkx>=2.3
        * pandas>=0.21
        * pydot
        * scanpy>=1.6
        * scikit-learn
        * scipy>=1.4
        * scprep
        * tslearn
        
        ### Install on Linux, Windows (WSL) and macOS
        Create a new environment for CAPITAL (recommended).
        ```
        $ conda create -n capital python=3.8 graphviz
        ```
        Next, activate the environment and pull CAPITAL from PyPI:
        ```
        $ conda activate capital
        $ pip install capital
        ```
        
        ## Usage
        Read the documentation (available very soon). CAPITAL uses a single-cell analysis toolkit [Scanpy](https://scanpy.readthedocs.io/en/latest/index.html) in its implementation so that one can also use Scanpy's useful functions including preprocessing, plotting and datasets in the CAPITAL environment.
        
        ## Reference
        Reiichi Sugihara, Yuki Kato, Tomoya Mori and Yukio Kawahara,
        **Alignment of time-course single-cell RNA-seq data with CAPITAL**,
        Preprint *bioRxiv* at [https://doi.org/10.1101/859751](https://doi.org/10.1101/859751), 2019.
        
        Reiichi Sugihara, Yuki Kato, Tomoya Mori and Yukio Kawahara,
        **Comparative pseudotime analysis of single-cell RNA-seq data with CAPITAL**,
        *submitted*.
        
        ---
        If you have any questions, please contact [Yuki Kato](http://www.med.osaka-u.ac.jp/pub/rna/ykato/en/)
        *Graduate School of Medicine, Osaka University, Japan*
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: BSD License
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Description-Content-Type: text/markdown
