Overview of the analysis | Installation | Interactive analysis using the DEP Shiny apps | Differential analysis | Example dataset: Ubiquitin interactors | Loading of the data | Data preparation | Generate a SummarizedExperiment object | Prerequisites of the SummarizedExperiment object | Filter on missing values | Normalization | Impute data for missing values | Differential enrichment analysis | Visualization of the results | PCA plot | Correlation matrix | Heatmap of all significant proteins | Volcano plots of specific contrasts | Barplots of a protein of interest | Frequency plot of significant proteins and overlap of conditions | Results table | Generate a data.frame from the resulting SummarizedExperiment object | Save your results object for reuse | Workflow functions for the entire analysis | LFQ-based DEP analysis | TMT-based DEP analysis | Session information

Overview of the analysis | Installation | Interactive analysis using the DEP Shiny apps | Differential analysis | Example dataset: Ubiquitin interactors | Loading of the data | Data preparation | Generate a SummarizedExperiment object | Prerequisites of the SummarizedExperiment object | Filter on missing values | Normalization | Impute data for missing values | Differential enrichment analysis | Visualization of the results | PCA plot | Correlation matrix | Heatmap of all significant proteins | Volcano plots of specific contrasts | Barplots of a protein of interest | Frequency plot of significant proteins and overlap of conditions | Results table | Generate a data.frame from the resulting SummarizedExperiment object | Save your results object for reuse | Workflow functions for the entire analysis | LFQ-based DEP analysis | TMT-based DEP analysis | Session information

Goal of this vignette | Simulate data | Generate intensity values | Introduce missing values | Generate a SummarizedExperiment | Filter proteins based on missing values | Visualize the extend of missing values | Filter options | Scaling and variance stabilization | Data imputation of missing data | Explore the pattern of missing values | Imputation options | Advanced imputation methods | Mixed imputation on proteins (rows) | Mixed imputation on samples (columns) | Test for differential expression | Number of identified differentially expressed proteins | ROC curves | Differences in response | Session information

Goal of this vignette | Simulate data | Generate intensity values | Introduce missing values | Generate a SummarizedExperiment | Filter proteins based on missing values | Visualize the extend of missing values | Filter options | Scaling and variance stabilization | Data imputation of missing data | Explore the pattern of missing values | Imputation options | Advanced imputation methods | Mixed imputation on proteins (rows) | Mixed imputation on samples (columns) | Test for differential expression | Number of identified differentially expressed proteins | ROC curves | Differences in response | Session information