Man pages for mathiaskalxdorf/IceR
Requantification of label-free DDA proteomics data pre-analyzed by MaxQuant.
| add_annotations | Adds sample annotation information to loaded MaxQuant or IceR... |
| add_isotope_features | Extend IceR features by expected +1-isotopic features |
| align_features | Perform alignment of pre-determined MS1-features by MaxQuant... |
| Barplots | Generate barplots |
| BarplotsSBS | Generate side-by-side barplots |
| Barplotsstacked | Generate stacked barplots |
| compare_general_numbers | Compare general numbers between data sets |
| convert_rawTIMS | Extract MS1-spectra from raw TIMS-ToF Pro data |
| densityplots | Density plots |
| determine_general_numbers | Determine general identification and quantification numbers |
| Heatmap | Heatmap visualization of data |
| LIMMA_analysis | Perform differential expression analysis using LIMMA |
| load_MaxQ_data | Load MaxQuant result files |
| load_Requant_data | Load IceR result files |
| maxDensity | Function to determine at which value a density maximum is... |
| mzxml_to_list | Prepare mzXML files for IceR workflow |
| normalize_data | Normalize quantification data |
| peak_decision | Peak decision algorithm only designed for internal use |
| Peak_selection_FDR | Peak selection FDR algorithm for internal use |
| PECA_analysis | Perform differential expression analysis using peptide-level... |
| plot_accuracy | Compare coefficients of variation of quantifications between... |
| requantify_features | Perform quantification of IceR features |
| runIceR | Start GUI of IceR |
| run_msconvert_raw_mzXML | Convert thermo raw files to mzXML with centroided ms1 scans... |
| SaveExcel | Save data.frames or list of data.frames as xlsx-files. |
| set_sample_names | Change sample (column) names of loaded MaxQuant or IceR data |
