Metadata-Version: 2.4
Name: cassiopeia-lineage
Version: 2.0.0
Summary: Single Cell Lineage Reconstruction with Cas9-Enabled Lineage Recorders
Home-page: https://github.com/YosefLab/Cassiopeia
Author-email: mattjones315@berkeley.edu
License: MIT license
Keywords: scLT
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
License-File: LICENSE
License-File: AUTHORS.rst
Requires-Dist: Biopython>=1.71
Requires-Dist: bokeh>=0.12.15
Requires-Dist: cython>=0.29.2
Requires-Dist: ete3>=3.1.1
Requires-Dist: hits
Requires-Dist: itolapi
Requires-Dist: matplotlib>=2.2.2
Requires-Dist: nbconvert>=5.4.0
Requires-Dist: nbformat>=4.4.0
Requires-Dist: networkx>=2.5
Requires-Dist: ngs-tools>=1.5.3
Requires-Dist: numba>=0.51.0
Requires-Dist: numpy>=1.19.5
Requires-Dist: pandas>=1.1.4
Requires-Dist: pysam>=0.14.1
Requires-Dist: python-Levenshtein
Requires-Dist: PyYAML>=3.12
Requires-Dist: scipy>=1.2.0
Requires-Dist: typing-extensions>=3.7.4
Requires-Dist: tqdm>=4
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

Cassiopeia: A pipeline for single-cell lineage tracing data
=============================================================

Cassiopeia is an end-to-end pipeline for single-cell lineage tracing experiments.
The software contained here comes equipped with modules for processing sequencing reads,
reconstructing & plotting trees, analyzing these trees, and benchmarking new algorithms.

You can find all of our [documentation here](https://cassiopeia-lineage.readthedocs.io/en/latest/index.html).

We also have provided tutorials for three modules:

- [processing fastqs](https://github.com/YosefLab/Cassiopeia/blob/master/notebooks/preprocess.ipynb)
- [reconstructing trees](https://github.com/YosefLab/Cassiopeia/blob/master/notebooks/reconstruct.ipynb)
- [simulating trees and benchmarking](https://github.com/YosefLab/Cassiopeia/blob/master/notebooks/benchmark.ipynb)


You can also find our originally describing Cassiopeia published in [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02000-8)) 

Free Software: MIT License

Installation
--------------

1. Clone the package as so: ``git clone https://github.com/YosefLab/Cassiopeia.git``

2. Ensure that you have python3.6 installed. You can install this via pip.

3. Make sure that Gurobi is installed. You can follow the instructions listed [here](http://www.gurobi.com/academia/for-universities). To verify that it's working correctly, use the following tests:
    * Run the command ``gurobi.sh`` from a terminal window
    * From the Gurobi installation directory (where there is a setup.py file), use ``python setup.py install --user``
    
4. Install Cassiopeia by running `make install` from the directory where you have Cassiopeia installed.
    
To verify that it installed correctly, try running our tests with `make test`.

Reference
----------------------

If you've found Cassiopeia useful for your research, please consider citing our paper published in Genome Biology:


Matthew G Jones*, Alex Khodaverdian*, Jeffrey J Quinn*, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonatahn S Weissman, Nir Yosef. (2020), [*Inference of single-cell phylogenies from lineage tracing data using Cassiopeia*](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02000-8), Genome Biology


