Package: systemPipeR
Type: Package
Title: systemPipeR: NGS workflow and report generation environment
Version: 1.26.2
Date: 2020-05-24
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
        RiboSeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
        GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology,
        ReportWriting, Workflow
Description: R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.
Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
        methods
Imports: GenomicRanges, GenomicFeatures (>= 1.31.3),
        SummarizedExperiment, VariantAnnotation (>= 1.25.11), rjson,
        ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate,
        pheatmap, batchtools, yaml, stringr, assertthat, magrittr, DOT,
        rsvg, IRanges, testthat
Suggests: BiocGenerics, ape, BiocStyle, knitr, rmarkdown, biomaRt,
        BiocParallel, BiocManager, systemPipeRdata, GenomicAlignments,
        grid, DT, dplyr, kableExtra
VignetteBuilder: knitr
SystemRequirements: systemPipeR can be used to run external
        command-line software (e.g. short read aligners), but the
        corresponding tool needs to be installed on a system.
License: Artistic-2.0
URL: https://systempipe.org/
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: RELEASE_3_13
git_last_commit: 18fdf17
git_last_commit_date: 2021-05-24
Date/Publication: 2021-05-25
NeedsCompilation: no
Packaged: 2021-05-25 22:34:59 UTC; biocbuild
Built: R 4.1.0; ; 2021-06-03 20:09:56 UTC; unix
