├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── Circos.R ├── batchQC.R ├── batchtest.R ├── correlation.R ├── heatmap.R ├── lmfitC.R ├── pca.R ├── shapeAnalysis.R ├── simulate_data.R ├── sva.R └── utils.R ├── README.md ├── data ├── example_batchqc_data.rda └── protein_example_data.rda ├── inst ├── CITATION ├── NEWS.Rd ├── example │ ├── batchqc_combat_adj_report.html │ ├── batchqc_pipeline.R │ └── batchqc_report.html ├── reports │ ├── batchQC.html │ ├── batchqc_report.Rmd │ └── libs │ │ └── bootstrap │ │ ├── css │ │ ├── bootstrap-responsive.min.css │ │ ├── bootstrap.min.css │ │ └── user.css │ │ ├── img │ │ ├── glyphicons-halflings-white.png │ │ └── glyphicons-halflings.png │ │ └── javascript │ │ ├── bootstrap.min.js │ │ ├── jquery-1.10.1.min.js │ │ └── user.js ├── rmarkdown │ └── templates │ │ └── batchqc │ │ ├── skeleton │ │ └── skeleton.Rmd │ │ └── template.yaml └── shiny │ └── BatchQC │ ├── server.R │ └── ui.R ├── man ├── BatchQCout-class.Rd ├── batchQC.Rd ├── batchQC_analyze.Rd ├── batchQC_condition_adjusted.Rd ├── batchQC_filter_genes.Rd ├── batchQC_fsva_adjusted.Rd ├── batchQC_num.sv.Rd ├── batchQC_shapeVariation.Rd ├── batchQC_sva.Rd ├── batchQC_svregress_adjusted.Rd ├── batchqc_circosplot.Rd ├── batchqc_correlation.Rd ├── batchqc_corscatter.Rd ├── batchqc_explained_variation.Rd ├── batchqc_heatmap.Rd ├── batchqc_pc_explained_variation.Rd ├── batchqc_pca.Rd ├── batchqc_pca_svd.Rd ├── batchtest.Rd ├── combatPlot.Rd ├── example_batchqc_data.Rd ├── getShinyInput.Rd ├── getShinyInputCombat.Rd ├── getShinyInputOrig.Rd ├── getShinyInputSVA.Rd ├── getShinyInputSVAf.Rd ├── getShinyInputSVAr.Rd ├── gnormalize.Rd ├── lmFitC.Rd ├── log2CPM.Rd ├── makeSVD.Rd ├── pcRes.Rd ├── plotPC.Rd ├── plot_genewise_moments.Rd ├── plot_samplewise_moments.Rd ├── protein_example_data.Rd ├── rnaseq_sim.Rd ├── setShinyInput.Rd ├── setShinyInputCombat.Rd ├── setShinyInputOrig.Rd ├── setShinyInputSVA.Rd ├── setShinyInputSVAf.Rd └── setShinyInputSVAr.Rd ├── tests ├── testthat.R └── testthat │ └── test_batchQC.R └── vignettes ├── BatchQCIntro.Rmd ├── BatchQC_examples.Rmd └── BatchQC_usage_advanced.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mani2012/BatchQC/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mani2012/BatchQC/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mani2012/BatchQC/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: 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