├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── IceR.Rproj ├── NAMESPACE ├── NEWS.md ├── R ├── Feature_alignment_requantification.R └── General.R ├── README.md ├── _config.yml ├── images ├── CV_quant.jpg ├── DE_results.jpg ├── General_numbers.jpg ├── IceR.jpg ├── IceR_gui.jpg ├── IceR_gui_QC_alignment.jpg ├── IceR_gui_QC_quantification.jpg └── Normalization.jpg ├── index.md ├── inst └── shiny │ └── IceR_UI │ └── app.R └── man ├── Barplots.Rd ├── BarplotsSBS.Rd ├── Barplotsstacked.Rd ├── Heatmap.Rd ├── LIMMA_analysis.Rd ├── PECA_analysis.Rd ├── Peak_selection_FDR.Rd ├── SaveExcel.Rd ├── add_annotations.Rd ├── add_isotope_features.Rd ├── align_features.Rd ├── compare_general_numbers.Rd ├── convert_rawTIMS.Rd ├── densityplots.Rd ├── determine_general_numbers.Rd ├── load_MaxQ_data.Rd ├── load_Requant_data.Rd ├── maxDensity.Rd ├── mzxml_to_list.Rd ├── normalize_data.Rd ├── peak_decision.Rd ├── plot_accuracy.Rd ├── requantify_features.Rd ├── runIceR.Rd ├── 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