README.md

PICASSO: Pipeline, Code and Analysis for Scalable Single-cell Omics

Temporarily designed for single-cell learning

Usage

Firstly, clone this repository.

mkdir ONE_DRIECTORY
cd ONE_DRIECTORY
git clone https://github.com/Moloch0/PICASSO.git
pwd # Gets the absolute path to the folder
DRIECTORY_OF_PICASSO

Then, if you want to use R scripts:

source(paste0("DRIECTORY_OF_PICASSO","/PICASSO/picasso.R"), chdir=TRUE)

file management and scripts usage

The file management system and the scripts usage system are synchronized. Here, the second-level header of the document is the pipeline, and the third-level header is the module. choose_pipeline("scrnaseq") loads all functions of that pipeline.

> choose_pipeline()
#choose_pipeline(<pipelie>,<module>)

#---- base ----#
--> plot 

#---- bulk_omics ----#
--> bulkrnaseq 
--> chipseq 

#---- other_bioinfo ----#
--> annotation 
--> functional_analysis 
--> sequence_analysis 

#---- sc_omics ----#
--> scrnaseq 
--> smartseq 
--> vdj 

#---- stastics ----#
--> clinical_analysis 
--> deep_learning 
--> experiment_analysis 
--> machine_learning 
Please specify a pipeline and press 'Enter'
scrnaseq # type the pipeline
This job starts at: 2023-04-16 23:35:52 
This script is in: /public/home/luoliheng/PICASSO 
Succeed to load script: scrnaseq
# Or
choose_pipeline("scrnaseq")

Acknowledgements

• 2023/4/16 Cao Jun first proposed building a pipeline for better scientific training. Luo Liheng created the github repository. Along with Zhang Xu who joined this repository, they were the original contributors.

Wish you all the best in bioinfomatics research!