celescope 1.6.0

Single Cell Analysis Pipelines

CeleScope

CeleScope is a collection of bioinfomatics analysis pipelines developed at Singleron to process single cell sequencing data generated with Singleron products. These pipelines take paired-end FASTQ files as input and generate output files which can be used for downstream data analysis as well as a summary of QC criteria.

Detailed docs can be found in manual.

Hardware/Software Requirements

• minimum 32GB RAM(to run STAR aligner)
• conda
• git

Installation

1. Clone repo

git clone https://github.com/singleron-RD/CeleScope.git

2. Create conda environment and install conda packages

cd CeleScope
conda create -n celescope -y --file conda_pkgs.txt

Alternatively, you can use mamba to improve speed.

conda install mamba
mamba create -n celescope -y --file conda_pkgs.txt

3. Install celescope

Make sure you have activated the celescope conda environment before running pip install celescope.

conda activate celescope
pip install celescope

Quick start