SPR WorkFlow Collection

Workflow Templates

systemPipeR project provides pre-configured workflows and reporting templates for a wide range of NGS applications that are listed bellow. The systemPipeR project provides a suite of R/Bioconductor packages for designing, building and running end-to-end analysis workflows on local machines, HPC clusters and cloud systems, while generating at the same time publication quality analysis reports.

systemPipeRdata is a helper package to generate with a single command workflow templates that are intended to be used by its parent package systemPipeR (H Backman and Girke 2016).

WorkFlowDescriptionVersionGitHubR-CMD-check
SPchipseqChIP-Seq Workflow TemplateStableR-CMD-check
SPriboseqRIBO-Seq Workflow TemplateStableR-CMD-check
SPrnaseqRNA-Seq Workflow TemplateStableR-CMD-check
SPvarseqVAR-Seq Workflow TemplateStableR-CMD-check
SPmethylseqMethyl-Seq Workflow TemplateExperimentalR-CMD-check
SPdenovoDe novo transcriptome assembly Workflow TemplateExperimentalR-CMD-check
SPclipseqCLIP-Seq Workflow TemplateExperimentalR-CMD-check
SPmetatransMetatranscriptomic Sequencing Workflow TemplateExperimentalR-CMD-check
SPatacseqATAC-Seq Workflow TemplateExperimentalR-CMD-check
SPpolyriboseqPolyribosomal RNA-Seq Workflow TemplateExperimentalR-CMD-check
SPhicHi-C Workflow TemplateExperimentalR-CMD-check
SPmirnaseqMicroRNA-Seq Workflow TemplateExperimentalR-CMD-check
SPblastBLAST Workflow TemplateExperimentalR-CMD-check
SPscrnaseqSingle-Cell RNA-Seq Workflow TemplateExperimentalR-CMD-check

Reference

H Backman, Tyler W, and Thomas Girke. 2016. “systemPipeR: NGS workflow and report generation environment.” BMC Bioinformatics 17 (1): 388. https://doi.org/10.1186/s12859-016-1241-0.

Existing templates

How to install systemPipe Workflows

Rules to create a new Workflow Template

Last modified 2022-06-08: Update create_param_v2.Rmd (ee1b9a7)