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Singleron-RD / CeleScope

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README.md

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
  1. 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
  1. Install celescope

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

conda activate celescope
pip install celescope

Quick start

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GEXSCOPE Single Cell Analysis Pipelines expand collapse
Python and 6 more languages
MIT
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