Single-Cell Analysis, comparing pseudotime trajectories with tree alignment
Project description
CAPITAL
Comparative pseudotime analysis of single-cell RNA-seq data
Last updated: 2021-03-16
We present CAPITAL, a computational method for comparing pseudotime trajectories with tree alignment whereby trajectories including branchings can be automatically compared.
Installation
- CAPITAL (ver. 1.0.2) in Python
Requirements
- Python>=3.8 (Miniconda 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. CAPITAL uses a single-cell analysis toolkit Scanpy in its implementation so that one can also use Scanpy's useful functions including preprocessing, plotting and datasets in the CAPITAL environment.
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