Introduction | Prepare Layout For Accommodating Multiple Smaller Plots | Optimal Legend Location | One More Histogram Function ... | Small Histogram(s) as Legend | Violin Plots | Paired Violin Plots | Plotting Sorted Values ('Summed Frequency') | Color-Code Numeric Content Of Matrix (Heatmap) | Examine Counts Based On Variable Threshold Levels (for ROC curves) | Compare Two Groups With Sub-Organisation Each | Plotting Linear Regression And Confidence Intervals | Principal Components Analysis (PCA) | PCA out of wrGraph | Label all points in PCA | MA-Plot | Volcano-Plot | Standalone html Page With Plot And Mouse-Over Interactive Features | Acknowledgements | Appendix: Session-Info

Introduction | Dependencies and Compilation | Installation And Loading | Speed Optimized Functions In The Package wrMisc | Assessing Basic Information About Variability (for matrix) | Data Organized In (Sub-)Groups As Sets Of Columns | Counting Number Of NAs Per Row And Group Of Columns | Fast NA-omit For Very Large Objects | Minimum Distance/Difference Between Values | Working With Lists (And Lists Of Lists) | Partial unlist | Appending/Combining Lists | rbind On Lists | cbind On Lists | Merge Multiple Matrices From List | Fuse Content Of List-Elements With Redundant (Duplicated) Names | Filtering Lines And/Or Columns For All List-Elements Of Same Size | Replacements In List | Organize Values Into List And Sort By Names | Batch-filter List-Elements | Transform Columns Of Matrix To List Of Vectors | Working With Arrays | CV (Coefficient Of Variance) With Arrays | Slice 3-dim Array In List Of Matrixes (Or Arrays) | Working With Redundant Data | Identify What Is Repeated (and Where Repeated Do Occur) | Correct Vector To Unique (While Maintaining The Original Vector Length) | Mark Any Duplicated (ie Ambiguous) Elements by Changing Their Names (and Separate from Unqiue) | Compare Multiple Vectors And Sort By Number Of Common/Repeated Values/Words | Combine Multiple Matrixes Where Some Column-Names Are The Same | Filter Matrix To Keep Only First Of Repeated Lines | Filter To Unique Column-Content Of Matrix, Add Counter And Concatenated Information | Get First Of Repeated By Column | Transform (ambigous) Matrix To Non-ambiguous Matrix (In Respect To Given Column) | Combine Replicates From List To Matrix | Combine Redundant Lines From List with (Multiple) Matrix According to Reference | Non-redundant Lines Of Matrix | Filter For Unique Elements /2 | Make Non-redundant Matrix | Example : Summarize table for longest of transcripts | Combine/Reduce Redundant Lines Based On Specified Column | Convert Matrix (eg With Redundant) Row-Names To data.frame | Find And Combine Points Located Very Close In X/Y Space | Bin And Summarize Values According To Their Names | Regrouping Simultaneaously by Two Factors | Batch Replacing Of Values Or Character-Strings | Multi-to-multi Matching Of (Concatenated) Terms | Comparing Global Patterns | Search For Similar (Numeric) Values | Find Similar Numeric Values Of Two Columns Of A Matrix | Find Similar Numeric Values From Two Vectors/Matrixes | Fuse Previously Identified Pairs To 'Clusters' | Eliminate Close (Overlapping) Points (In Bivariate x & y Space) | Mode Of (Continuous) Data | Most Frequently Occuring Value (traditional mode) | Text-Manipulations | Protect Special Characters | Trimming Redundant Text | Removing Redundant/Shared Words | Extract Common Part Of Text | Manipulating Enumerator-Extensions | Remove/Modify Enumerators | Unify Enumerators | Find/Choose Column Most Likely Containing Sample-Names | Find Common Unit | Adjust Decimal Prefixes And Extact Numeric+Unit Part | Merging Multiple Named Vectors To Matrix | Match All Lines of Matrix To Reference Note | Order Matrix According To Reference | Value Matching With Option For Concatenated Terms | Check for (Strict) Order | Working With Regressions | Best Starting Point For Linear Regressions (Start of linearity) | High Throughput Testing For Linear Regressions | Combinatorics Issues | All Pairwise Ratios | Count Frequency Of Terms Combined From Different Drawings (combineAsN) | Import/Export | Batch-Reading Of CSV Files | Batch-Reading Of Tabulated Files | Reading/Importing Incomplete Tables | Converting Url For Reading Tabulated Data From GitHub | Data Vectorization | Normalization | Filter Lines Of Matrix To Reduce Content Of NAs | Filter For Each Group Of Columns For Sufficient Data As Non-NA | Filter As Separate Pairwise Groups Of Samples | Cleaning Replicates | The Function normalizeThis() | Normalize By Rows | Matrix Coordinates Of Values/Points According To Filtering | Trimmed Mean | Blockwise Normalization Of 2 or 3 Data-Sets | Statistical Testing | Normal Random Number Generation with Close Fit to Expected mean and sd | Moderated Pair-Wise t-Test from limma | Multiple Moderated Pair-Wise t-Tests From limma | Choosing amongst multiple possible pairwise comparisons | Transform p-values To Local False Discovery Rate (lfdr) | Confindence Intervals (under Normal Distribution) | Extract Groups Of Replicates From Pair-Wise Column-Names | Extract Numeric Part Of Column-Names | Automatic Determination Of Replicate Structure Based On Meta-Data | Addressing Pairwise Comparisons | Suggesting A Separator For Pairwise Combinations | Identify The Separator Used In Concatenated Text | Working With Clustering | Prepare Data For Clustering | Characterize Clustering Results | Remove or Reassign Orphans | Tree-Like Structures | Filter Lists Of Connected Nodes, Extension Of Networks As 'Sandwich' | Convert Collection Of Pairs Of Nodes To Propensity Matrix | Characterize Individual Contribution Of Single Edges In Tree-Structures | Count Same Start- And End- Sites Of Edges (Or Fragments) | Support for Graphical Output | Convenient Paste-Collapse | Transform Numeric Values to Color-Gradient | Assign New Transparency To Given Colors | Print Matrix-Content As Plot | Other Convenience Functions | Writing Compact Dates (more options ...) | Acknowledgements | Session-Info

Introduction | Experimental Setup For Benchmark Tests | The Ramus Data-Set | Meta-Data Describing The Experiment (sdrf) | Key Elements And Additional Functions | Protein Identification and Initial Quantification | MaxQuant | ProteomeDiscoverer | Proline | Further Preparation Of Data | Basic Data Treatment | Structure of Experiment | Normalization | Presence of NA-values | NA-Imputation and Statistical Testing for Changes in Abundance | Analysis Using All Proteins Identified (Matrix + UPS1) | Pairwise Testing Summary | Volcano Plots | ROC for Multiple Pairs | Grouping of ROC Curves to Display Representative Ones | Plotting ROC Curves for the Best Cluster (the '+++++') | ROC Curves for 2nd Best Cluster (the '++++') | ROC Curves for the 3rd Best Cluster (the '+++') | ROC Curves for the 4th Best Cluster (the '++') | ROC Curves for the Weakest Cluster 1 (the '+') | Analysis Focussing on UPS1 Spike-In Proteins Only | Similarity by PCA (UPS1 proteins only) | PCA of UPS1 for ProteomeDiscoverer | PCA of UPS1 for MaxQuant | PCA of UPS1 for Proline | CV of Replicates | Testing All Individual UPS1 Proteins By Linear Regression | Linear Regression for each UPS1 : ProteomeDiscoverer | Linear Regression for each UPS1 : MaxQuant | Linear Regression for each UPS1 : Proline | Frequency Of Starting Levels For Regression | Global Comparison Of Regression Models | Summarize Linear Regression Results | Grouping of UPS1 Proteins to Display Representative Proteins | Representative UPS1-protein of the Best Group (the '+++++') | Representative UPS1-protein of the 2nd Best Group (the '++++') | Representative UPS1-protein of the 3rd Group (the '+++') | Representative UPS1-protein of the 4th Group (the '++') | Representative UPS1-protein of the 5th (And Last) Group (the '+') | Additional Comments | Acknowledgements | Session-Info

Introduction | Calculating Molecular Masses From Composition Formulas | Molecular masses based on (summed) chemical formulas | Molecular masses based on amino-acid sequence | Working With Fasta(Files) | Reading Fasta Files (from Uniprot) | Writing Sequences As Fasta Files | Analyzing Label-Free Quantitative Proteomics Data | Label-free Quantitative Proteomics Introduction | Import From Dedicated Quantification Algorithms/Software | MaxQuant: Import Protein Quantification Data | Adding Meta-Data at Import (Example MaxQuant) | Adding Experimental Setup (Sdrf) to Meta-Data at Import (Example MaxQuant) | Exporting Experimental Setup from MaxQuant to Draft-Sdrf | MaxQuant : Import Peptide Data | ProteomeDiscoverer : Import Protein Quantification | ProteomeDiscoverer : Import Peptide Data | DIA-NN: Import Protein Quantification Data | DIA-NN : Import Peptide Data | Proline : Import Protein Quantification Data | Fragpipe : Import Protein Quantification Data | MassChroQ : Import Protein Quantification Data | AlphaPept : Import Protein Quantification Data | Ionbot : Import Peptide Identification And Quantification Data | Wombat-P : Import Protein Quantification Data | OpenMS : Import Protein Quantification Data | Importing Sdrf Meta-Data | Removing Samples From Proteomics Projects | Combining Proteomics Projects | Normalization | Imputation of NA-values | Filtering | Statistical Testing | Data Exploration With Graphical Support | PCA | MA-plot | Volcano-Plot | Reporting Results | Further Steps | Protein Annotation | Appendix | Acknowledgements | Session-Info

Introduction | Nomenclature | Obtaining Molecular Mass For Chemical Structures (using wrProteo) | Molecular Mass Of Peptides And Proteins | Fragmenting Peptide/Protein -Sequences | Fragmenting a Protein Sequence | Example 1 : Single Peptide Fragmentation and Comparison To Prospector | Example 2 : A Detailed Toy Example For Predicting Fragments | Terminal Fragments | Internal Fragments | Fixed And Variable Modifications | Basic Identification Including Fixed Modifications | Tolerance | Identification Example | Final Thoughts For Calculating Fragments | Acknowledgements | Appendix: Session-Info