Package: BatchQC
Type: Package
Title: Batch Effects Quality Control Software
Version: 1.28.0
Date: 2020-10-11
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 (>= 3.5.0)
Collate: 'simulate_data.R' 'heatmap.R' 'pca.R' 'batchtest.R'
        'batchQC.R' 'correlation.R' 'utils.R' 'sva.R' 'Circos.R'
        'shapeAnalysis.R' 'lmfitC.R'
Suggests: testthat
Imports: utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
        corpcor, moments, matrixStats, ggvis, heatmaply, reshape2,
        limma, grDevices, graphics, stats, methods, Matrix
biocViews: BatchEffect, GraphAndNetwork, Microarray,
        PrincipalComponent, Sequencing, Software, Visualization,
        QualityControl, RNASeq, Preprocessing, DifferentialExpression,
        ImmunoOncology
SystemRequirements: pandoc (http://pandoc.org/installing.html) for
        generating reports from markdown files.
VignetteBuilder: knitr
RoxygenNote: 7.1.0
NeedsCompilation: no
Packaged: 2023-04-26 00:28:09 UTC; biocbuild
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/BatchQC
git_branch: RELEASE_3_17
git_last_commit: d0af9be
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Built: R 4.3.0; ; 2023-04-26 15:16:52 UTC; windows
