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 |
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SPchipseq | ChIP-Seq Workflow Template | ![]() |
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SPriboseq | RIBO-Seq Workflow Template | ![]() |
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SPrnaseq | RNA-Seq Workflow Template | ![]() |
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SPvarseq | VAR-Seq Workflow Template | ![]() |
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SPmethylseq | Methyl-Seq Workflow Template | ![]() |
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SPdenovo | De novo transcriptome assembly Workflow Template | ![]() |
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SPclipseq | CLIP-Seq Workflow Template | ![]() |
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SPmetatrans | Metatranscriptomic Sequencing Workflow Template | ![]() |
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SPatacseq | ATAC-Seq Workflow Template | ![]() |
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SPpolyriboseq | Polyribosomal RNA-Seq Workflow Template | ![]() |
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SPhic | Hi-C Workflow Template | ![]() |
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SPmirnaseq | MicroRNA-Seq Workflow Template | ![]() |
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SPblast | BLAST Workflow Template | ![]() |
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SPscrnaseq | Single-Cell RNA-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.