ImputeHiFI

ImputeHiFI: an imputation method for single-cell multiplexed DNA FISH data by utilizing single-cell Hi-C and RNA FISH data

ImputeHiFI has three modes to accommodate different data scenarios.

The workflow of ImputeHiFI mode 1.

Installation instructions

Dependences

• Python 3.9

• scanpy

• pandas

• numpy

• tqdm

• scipy

• matplotlib

• seaborn

• portalocker

Installation

Method1: to install the conda environment

Step1:

git clone https://github.com/zhanglabtools/ImputeHiFI
cd ImputeHiFI

Step2:

conda env create --name ImputeHiFI -f environment.yml

Step3:

conda activate ImputeHiFI

In this environment, all the need of ImputeHiFI have been installed.

Method2: install from Pypi

pip install ImputeHiFI

Documentation

See Tutorial_run_ImputeHiFI.ipynb for the usage of ImputeHiFI.

The data used in the tutorial can be downloaded here.

Contact information

More information please contact Shichen Fan at 2784225493@qq.com.

References

If ImputeHiFI is used in your research, please cite our paper:

ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data