About Project

Overview

The systemPipe project provides a suite of R/Bioconductor packages for designing, building, and executing end-to-end data analysis workflows on local machines and high-performance computing (HPC) systems, while simultaneously generating publication-quality analysis reports.

This website serves primarily as a landing page that provides a high-level overview of each package and links to their corresponding pages on Bioconductor. Detailed usage instructions, examples, and technical documentation are available in the package vignettes hosted on Bioconductor (linked below).

Core Packages

systemPipeR is the core workflow management package of the project. It enables users to define, organize, and execute workflows that integrate R-based analysis with external command-line software (H Backman and Girke 2016). An automated scientific reporting framework is an integral component of the package, supporting reproducible and transparent analyses. To simplify deployment and maximize reproducibility, systemPipeR is available as a Docker image on Docker Hub here.

systemPipeRdata provides a collection of pre-configured workflow templates and associated resources that simplify the setup of common analysis pipelines and serve as starting points for reproducible workflow development.

systemPipeShiny offers a Shiny-based graphical user interface for a subset of systemPipeR functionalities, along with interactive visualization tools for result exploration, post-processing, and figure assembly.

Workflow Templates

The systemPipeRdata package supplies pre-configured workflow templates that are fully compatible with systemPipeR. These templates include CWL parameter files for command-line steps and, in many cases, example datasets. They are designed to:

• reduce the learning curve,
• facilitate rapid testing of workflows, and
• provide modular building blocks for custom analyses.

Templates are available via systemPipeRdata on Bioconductor and from the project’s GitHub repositories. The table below lists the core workflows and links for accessing them.

Name	Description	URL
new	Generic Workflow Template	Bioc, GitHub
rnaseq	RNA-Seq Workflow Template	Bioc, GitHub
riboseq	RIBO-Seq Workflow Template	Bioc, GitHub
chipseq	ChIP-Seq Workflow Template	Bioc, GitHub
varseq	VAR-Seq Workflow Template	Bioc, GitHub
blast (SPblast)	BLAST Workflow Template	Bioc, GitHub
cheminfo (SPcheminfo)	Cheminformatics Drug Similarity Template	Bioc, GitHub
scrna (SPscrna)	Basic Single-Cell Workflow Template	Bioc, GitHub

Shared components used by some or all of the above workflows are given in this table. The param component is required for all workflows, while data is only used by some of them.

Name	Description	URL
param	CWL Parameter Files	GitHub
data	Small Test Datasets	GitHub