Package: systemPipeR
Type: Package
Title: systemPipeR: NGS workflow and report generation environment
Version: 2.6.0
Date: 2022-08-24
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, SummarizedExperiment, ggplot2, yaml, stringr,
        magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata,
        GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
        AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
        rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
        GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11)
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/, https://github.com/tgirke/systemPipeR
git_url: https://git.bioconductor.org/packages/systemPipeR
git_branch: RELEASE_3_17
git_last_commit: c8b1f6b
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-26 05:40:04 UTC; biocbuild
Built: R 4.3.0; ; 2023-04-26 16:31:39 UTC; windows
