Package: DEqMS 1.31.0

Overview of DEqMS | Quick start | Differential protein expression analysis with DEqMS using a protein table | Download and Read the input protein table | Extract quant data columns for DEqMS | Make design table. | Make contrasts | DEqMS analysis | Visualize the fit curve - variance dependence on quantified PSM | Extract the results as a data frame and save it | Make volcanoplot | DEqMS analysis using MaxQuant outputs (label-free data) | Read protein table as input and filter it | Make a data frame of unique peptide count per protein | DEqMS analysis on LFQ data | Visualize the fit curve | Extract outputs from DEqMS | DEqMS analysis using a PSM table (isobaric labelled data) | Read PSM table input | Summarization and Normalization | PSM/Peptide profile plot | Comparing DEqMS to other methods | Compare the variance estimate in DEqMS and Limma | Prior variance comparison between DEqMS and Limma | Residual plot for DEqMS and Limma | Posterior variance comparison between DEqMS and Limma | Compare p-values from DEqMS to ordinary t-test, ANOVA and Limma | T-test analysis | Anova analysis | Limma | Visualize the distribution of p-values by different analysis