systemPipeR statistics

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chevron_left Bioinformatics workflows Read alignment Differential expression Normalization Known transcript quantification Bioinformatics workflows Transcriptome annotation Data preprocessing chevron_right
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systemPipeR specifications


Unique identifier OMICS_09105
Name systemPipeR
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
limma, methods, grid, BiocGenerics, GenomicRanges, Biostrings, BiocStyle, SummarizedExperiment, edgeR, ggplot2, BiocParallel, DESeq2, RUnit, biomaRt, rmarkdown, knitr, GO.db, annotate, GOstats, pheatmap, rjson, Rsamtools(>=1.31.2), GenomicFeatures(>=1.31.3), BatchJobs, ape, VariantAnnotation(>=1.25.11), ShortRead(>=1.37.1)
Maintained Yes


No version available



  • person_outline Thomas Girke

Publication for systemPipeR

systemPipeR citations


Characterization and metabolic synthetic lethal testing in a new model of SDH loss familial pheochromocytoma and paraganglioma

PMCID: 5814199
PMID: 29464059
DOI: 10.18632/oncotarget.23639
call_split See protocol

[…] puting Facility Beowulf-style Linux cluster. SAM files were then converted to BAM file format using SAMtools [], and FPKM quantitation of individual transcript abundance was performed using R package systemPipeR [], available through the Bioconductor project. The resulting processed gene expression datasets are available via NCBI Gene Expression Omnibus (GEO) under entry GSE103662. […]


Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria

BMC Evol Biol
PMCID: 5715807
PMID: 29202688
DOI: 10.1186/s12862-017-1087-8

[…] were quantitated by Qubit analysis, multiplexed and sequenced on an Illumina HiSeq2500, except for the 1.5-day tuber sample which was sequenced on an Illumina NextSeq500. Data was analyzed using the systemPipeR workflow and report generation environment []. This included filtering and trimming reads using ShortRead, and aligning reads to the reference genome [] using Bowtie 2.2.5 and Tophat 2.0.1 […]


Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

PMCID: 5704230
PMID: 29125533
DOI: 10.3390/genes8110317

[…] st v. 20170302 with options for MCL clustering “-M”, report all clusters “-t 0”, and report gene composition analysis “-c” []. A Venn diagram of shared gene clusters was generated using the R package systemPipeR []. GO term enrichment of core genes found in all analyzed taxa was determined using GOseq.Sequenced Illumina paired reads and assembled transcripts were submitted to the NCBI SRA and TSA […]


Global analysis of ribosome associated noncoding RNAs unveils new modes of translational regulation

Proc Natl Acad Sci U S A
PMCID: 5699049
PMID: 29087317
DOI: 10.1073/pnas.1708433114
call_split See protocol

[…] hment analysis of GO terms was performed with the Classification SuperViewer tool ( Translational efficiency of protein-coding genes and other ribo-seq statistics were obtained using systemPipeR (). uORFs were predicted from 5′-UTR sequences from Araport 11 () with the predORF function using ATG as start codon and ≥60 nt. RFs on uORFs and mORFs were determined as in ref. . For gen […]


Transcriptome Analysis of Circulating Immune Cell Subsets Highlight the Role of Monocytes in Zaire Ebola Virus Makona Pathogenesis

Front Immunol
PMCID: 5662559
PMID: 29123522
DOI: 10.3389/fimmu.2017.01372
call_split See protocol

[…] Data analysis was performed with the RNA-Seq workflow module of the systemPipeR package available on Bioconductor (). RNA-Seq reads were demultiplexed, quality filtered, and trimmed using Trim Galore with an average phred score cutoff of 30 and minimum length of 75bp. […]


Infection with the Makona variant results in a delayed and distinct host immune response compared to previous Ebola virus variants

Sci Rep
PMCID: 5574898
PMID: 28852031
DOI: 10.1038/s41598-017-09963-y

[…] Data analysis was performed with the RNA-Seq workflow module of the systemPipeR package available on Bioconductor as previously described. RNA-Seq reads were trimmed using Trim Galore with an average phred score cutoff of 30 and minimum length of 75 bp; 3 bp from the […]

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systemPipeR institution(s)
Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
systemPipeR funding source(s)
This work was supported by grants from the National Science Foundation (ABI-0957099, MCB-1021969, IOS-1546879), the National Institutes of Health (U24AG051129, R01-AI36959) and the National Institute of Food and Agriculture (2011-68004-30154).

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