systemPipeR protocols

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systemPipeR specifications

Information


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
Requirements
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

Versioning


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Documentation


Maintainer


  • person_outline Thomas Girke <>

Publication for systemPipeR

systemPipeR in pipelines

 (3)
2017
PMCID: 5372813
PMID: 28424687
DOI: 10.3389/fimmu.2017.00335

[…] and thomas girke for assistance with rna-seq analysis. the authors would also like to acknowledge jonas töle for the mouse brain schematic in supplementary figure ., 1https://github.com/tgirke/systempiper., 2http://www.bioinformatics.babraham.ac.uk/projects/fastqc/., 3http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/., the authors received generous support from the following […]

2017
PMCID: 5662559
PMID: 29123522
DOI: 10.3389/fimmu.2017.01372

[…] were subjected to single-end 100 base pair sequencing using the illumina hiseq2500 platform (illumina, san diego, ca, usa)., 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 […]

2017
PMCID: 5814199
PMID: 29464059
DOI: 10.18632/oncotarget.23639

[…] 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., cell pellets […]


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systemPipeR in publications

 (6)
PMCID: 5704230
PMID: 29125533
DOI: 10.3390/genes8110317

[…] 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 […]

PMCID: 5699049
PMID: 29087317
DOI: 10.1073/pnas.1708433114

[…] analysis of go terms was performed with the classification superviewer tool (bar.utoronto.ca). 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. . […]

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

[…] article were submitted to the national center for biotechnology information sequence read archive (accession number prjna398558)., 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 […]

PMCID: 5504791
PMID: 28697735
DOI: 10.1186/s12929-017-0349-5

[…] with ~350 bp, which was sufficient to cover the entire complementarity-determining region (cdr) 3. in addition, the read length distribution was visualized using the seefastqplot function in the systempiper package (additional file )., the resulting fasta files were subjected to cdr3β extraction, v, d, and j regions mapping, clonotype identification of pcr, and sequencing errors with using […]

PMCID: 5430516
PMID: 28428619
DOI: 10.1038/s41598-017-01032-8

[…] 2100 bioanalyzer. multiplexed libraries were subjected to single-end 100 bp sequencing using the illumina hiseq2500 platform., 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. three base pairs from the 5′ end were trimmed as per clontech’s instruction and 30 bp […]


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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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