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).

WorkFlow Description Version GitHub R-CMD-check
systemPipeChIPseq ChIP-Seq Workflow Template Stable R-CMD-check
systemPipeRIBOseq RIBO-Seq Workflow Template Stable R-CMD-check
systemPipeRNAseq RNA-Seq Workflow Template Stable R-CMD-check
systemPipeVARseq VAR-Seq Workflow Template Stable R-CMD-check
systemPipeMethylseq Methyl-Seq Workflow Template Experimental R-CMD-check
systemPipeDeNovo De novo transcriptome assembly Workflow Template Experimental R-CMD-check
systemPipeCLIPseq CLIP-Seq Workflow Template Experimental R-CMD-check
systemPipeMetaTrans Metatranscriptomic Sequencing Workflow Template Experimental R-CMD-check
systemPipeATACseq ATAC-Seq Workflow Template Experimental R-CMD-check
systemPipePolyRIBOseq Polyribosomal RNA-Seq Workflow Template Experimental R-CMD-check
systemPipeHiC Hi-C Workflow Template Experimental R-CMD-check
systemPipemiRNAseq MicroRNA-Seq Workflow Template Experimental R-CMD-check
systemPipeBLAST BLAST Workflow Template Experimental R-CMD-check
systemPipescRNAseq Single-Cell RNA-Seq Workflow Template Experimental R-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.