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).

For stable workflows, one can directly use following to create/check supported workflows. When you typed the wrong/unsupported workflow names, all possible workflows will be listed. The table below also displays workflow template development status.

#> Error in systemPipeRdata::genWorkenvir("") : 
#>  workflow can only be assigned one of: chipseq, new, riboseq, rnaseq, varseq, SPblast, SPcheminfo, SPscrna
WorkFlow Description Version GitHub
SPchipseq ChIP-Seq Workflow Template Stable
SPriboseq RIBO-Seq Workflow Template Stable
SPrnaseq RNA-Seq Workflow Template Stable
SPvarseq VAR-Seq Workflow Template Stable
SPscrnaseq Single-Cell RNA-Seq Workflow Template Stable
SPblast BLAST Workflow Template Stable
SPcheminfo Basic drug discovery workflow Stable
SPmethylseq Methyl-Seq Workflow Template Experimental
SPdenovo De novo transcriptome assembly Workflow Template Experimental
SPclipseq CLIP-Seq Workflow Template Experimental
SPmetatrans Metatranscriptomic Sequencing Workflow Template Experimental
SPatacseq ATAC-Seq Workflow Template Experimental
SPpolyriboseq Polyribosomal RNA-Seq Workflow Template Experimental
SPhic Hi-C Workflow Template Experimental
SPmirnaseq MicroRNA-Seq Workflow Template Experimental


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.

Last modified 2021-08-05 : wf imgs (d7345620)