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
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.