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Single-Cell Analysis, comparing pseudotime trajectories with tree alignment

Project description

PyPI version Documentation Status

CAPITAL

Comparative pseudotime analysis of single-cell RNA-seq data

Last updated: 2021-12-03

We present CAPITAL, a computational method for comparing pseudotime trajectories with tree alignment whereby trajectories including branchings can be automatically compared.

Installation

  • CAPITAL (ver. 1.0.4) 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==1.8.1
  • 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.

Project details


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