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.

systemPipeRdata::genWorkflowEnv("")
#> 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
SPriboseq	RIBO-Seq Workflow Template
SPrnaseq	RNA-Seq Workflow Template
SPvarseq	VAR-Seq Workflow Template
SPscrnaseq	Single-Cell RNA-Seq Workflow Template
SPblast	BLAST Workflow Template
SPcheminfo	Basic drug discovery workflow
SPmethylseq	Methyl-Seq Workflow Template
SPdenovo	De novo transcriptome assembly Workflow Template
SPclipseq	CLIP-Seq Workflow Template
SPmetatrans	Metatranscriptomic Sequencing Workflow Template
SPatacseq	ATAC-Seq Workflow Template
SPpolyriboseq	Polyribosomal RNA-Seq Workflow Template
SPhic	Hi-C Workflow Template
SPmirnaseq	MicroRNA-Seq Workflow Template

Reference