DESCRIPTION

Package: systemsbio
Type: Package
Title: Streamlined Analysis and Integration of Systems Biology Data
Version: 0.5.0
Author: Frank Ruehle [aut, cre]
Maintainer: Frank Ruehle <f.ruehle@imb-mainz.de>
Description: This package consists of modularized wrapper functions for multiple genomics 
    analysis packages. It is designed for analysis of expression, methylation 
    and/or genotyping data. All modules can also be used individually. 
    E.g. for gene expression data, workflow is as follows: Illumina
    microarray data or custom microarray data are loaded into an Expressionet object
    and are normalised and QC-controlled. Limma package is used for differential
    expression analysis of all indicated group comparisons. Differential expressed
    genes are analysed for enriched GO terms, KEGG pathways and transcription factor
    binding sites using clusterProfiler and PWMEnrich. Principal component analysis
    and whole genome coexpression network analysis is performed using WGCNA and
    pcaGoPromoter packages. 
License: GPL-3
LazyData: TRUE
URL: https://github.com/frankRuehle/systemsbio.git
Encoding: UTF-8
Depends:
    R (>= 3.5.0)
biocViews:
Imports:
    beadarray,
    Biobase,
    ggplot2,
    gplots,
    gridSVG,
    knitr,
    plyr
Suggests:
    arrayQualityMetrics,
    BiocManager,
    BiocGenerics,
    clusterProfiler,
    DESeq2,
    DOSE,
    EDASeq,
    enrichplot,
    flashClust,
    GenomeInfoDb,
    GenomicFeatures,
    GenomicRanges,
    Hmisc,
    limma,
    MASS,
    minfi,
    MotifDb,
    pathview,
    pcaGoPromoter,
    PWMEnrich,
    ReactomePA,
    printFlush,
    rmarkdown,
    rgl,
    rJava,
    R.utils,
    seqLogo,
    SummarizedExperiment,
    VennDiagram,
    WGCNA
VignetteBuilder: knitr
RoxygenNote: 7.0.1