Statistical Analysis of Proteomic Data

1. Unveiling the Links between Peptide Identification and Differential Analysis FDR Controls by Means of a Practical Introduction to Knockoff Filters Lucas Etourneau, Nelle Varoquaux, and Thomas Burger 2. A Pipeline for Peptide Detection Using Multiple Decoys Syamand Hasam, Kristen Emery, William Stafford Noble, and Uri Keich 3. Enhanced Proteomic Data Analysis with MetaMorpheus Rachel M. Miller, Robert J. Millikin, Zach Rolfs, Michael R. Shortreed, and Lloyd M. Smith 4. Validation of MS/MS Identifications and Label-Free Quantification Using Proline Veronique Dupierris, Anne-Marie Hesse, Jean-Philippe Menetrey, David Bouyssie, Thomas Burger, Yohann Coute, and Christophe Bruley 5. Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler Matthew The and Lukas Kall 6. Left-Censored Missing Value Imputation Approach for MS-Based Proteomics Data with Gsimp Runmin Wei and Jingye Wang 7. Towards a More Accurate Differential Analysis of Multiple Imputed Proteomics Data with mi4limma Marie Chion, Christine Carapito, and Frederic Bertrand 8. Uncertainty Aware Protein-Level Quantification and Differential Expression Analysis of Proteomics Data with seaMass Alexander M. Phillips, Richard D. Unwin, Simon J. Hubbard, and Andrew W. Dowsey 9. Statistical Analysis of Quantitative Peptidomics and Peptide-Level Proteomics Data with Prostar Marianne Tardif, Enora Fremy, Anne-Marie Hesse, Thomas Burger, Yohann Coute, and Samuel Wieczorek 10. msmsEDA and msmsTests: Label-Free Differential Expression by Spectral Counts Josep Gregori, Alex Sanchez, and Josep Villanueva 11. Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts Lauriane Kuhn, Timothee Vincent, Philippe Hammann, and Helene Zuber 12. Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells Quentin Giai Gianetto 13. Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ Robert J. Millikin, Michael R. Shortreed, Mark Scalf, and Lloyd M. Smith 14. Robust Prediction and Protein Selection with Adaptive PENSE David Kepplinger and Gabriela V. Cohen Freue 15. Multivariate Analysis with the R Package mixOmics Zoe Welham, Sebastien Dejean, and Kim-Anh Le Cao 16. Integrating Multiple Quantitative Proteomic Analyses Using MetaMSD So Young Ryu, Miriam P. Yun, and Sujung Kim 17. Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data Jemma X. Wu, Dana Pascovici, Yunqi Wu, Adam K. Walker, and Mehdi Mirzaei