DNBC4 scRNA QC
Project description
DNBC4tools
An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
Introduction
- Propose
- An open source and flexible pipeline to analyze DNBelab C SeriesTM single-cell RNA datasets.
- Language
- Python3 and R scripts.
- Hardware/Software requirements
- x86-64 compatible processors.
- require at least 50GB of RAM and 4 CPU.
- centos 7.x 64-bit operating system (Linux kernel 3.10.0, compatible with higher software and hardware configuration).
Installation
installation manual
Install miniconda and creat DNBC4tools environment
- Git clone
git clone https://github.com/lishuangshuang0616/DNBC4tools.git
- Install miniconda3
wget -nv https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh -b -p $PATH
- Creat DNBC4tools environment
cd DNBC4tools
source /miniconda3/bin/activate
conda env create -f DNBC4tools_conda.yaml -n DNBC4tools
- Install R package that cannot be installed using conda
conda activate DNBC4tools
Rscript -e "devtools::install_github(c('chris-mcginnis-ucsf/DoubletFinder','ggjlab/scHCL','ggjlab/scMCA'),force = TRUE);"
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DNBC4-test-1.0.7.tar.gz
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