BatchQC/DESCRIPTION at master · tfaits/BatchQC · GitHub

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Package: BatchQC
Type: Package
Title: Batch Effects Quality Control Software
Version: 0.99.3
Date: 2016-03-23
Maintainer: Solaiappan Manimaran <manimaran_1975@hotmail.com>
Description: Sequencing and microarray samples often are collected or processed
    in multiple batches or at different times. This often produces technical
    biases that can lead to incorrect results in the downstream analysis.
    BatchQC is a software tool that streamlines batch preprocessing and
    evaluation by providing interactive diagnostics, visualizations, and
    statistical analyses to explore the extent to which batch variation impacts
    the data. BatchQC diagnostics help determine whether batch adjustment needs
    to be done, and how correction should be applied before proceeding with a
    downstream analysis. Moreover, BatchQC interactively applies multiple common
    batch effect approaches to the data, and the user can quickly see the
    benefits of each method. BatchQC is developed as a Shiny App. The output is
    organized into multiple tabs, and each tab features an important part of the
    batch effect analysis and visualization of the data. The BatchQC interface
    has the following analysis groups: Summary, Differential Expression,
    Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape,
    ComBat and SVA.
Author: Solaiappan Manimaran <manimaran_1975@hotmail.com>,
    W. Evan Johnson <wej@bu.edu>,
    Heather Selby <selbyh@bu.edu>,
    Claire Ruberman <claireruberman@gmail.com>,
    Kwame Okrah <kwame.okrah@gmail.com>,
    Hector Corrada Bravo <hcorrada@gmail.com>
URL: https://github.com/mani2012/BatchQC
BugReports: https://github.com/mani2012/BatchQC/issues
License: GPL (>= 2)
Depends: R (>= 3.2.0)
Collate:
    'simulate_data.R'
    'heatmap.R'
    'pca.R'
    'batchtest.R'
    'batchQC.R'
    'correlation.R'
    'utils.R'
    'sva.R'
    'Circos.R'
    'shapeAnalysis.R'
Suggests:
    testthat
Imports:
    utils,
    rmarkdown,
    knitr,
    pander,
    gplots,
    MCMCpack,
    shiny,
    sva,
    corpcor,
    moments,
    matrixStats,
    ggvis,
    d3heatmap,
    reshape2,
    limma,
    grDevices,
    graphics,
    stats
biocViews: BatchEffect, GraphAndNetwork, Microarray, PrincipalComponent,
    Sequencing, Software, Visualization, QualityControl, RNASeq, Preprocessing,
    DifferentialExpression
SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating
    reports from markdown files.
VignetteBuilder: knitr
RoxygenNote: 5.0.1