Man pages for LeoStafu/metaDAF
Metagenomics tools for detecting Differentially Abundant Features
| boxplot_AUC | Boxplot of AUC distribution across repetitions |
| boxplot_rank | Plot the distribution of the rank accross methods |
| build_DAF_data | Load all data for DAF analysis |
| curve_plot | Plot a ROC or PR curve |
| generate_curve_data | Compute metrics needed for ROC and PR curves |
| generate_differences | Generate artificial dataset with differences between 2 groups |
| generate_repeated_DAF_data | Generate several dataset for DAF analysis |
| HMP_2012_metadata | HMP 2012 metadata |
| HMP_2012_table_count | HMP 2012 table count |
| preprocess_DAF_data | Filter DAF data |
| process_ALDEx2 | Process the DAF analysis through the ALDEx2 package |
| process_DESeq2 | Process the DAF analysis through the DESeq2 package |
| process_edgeR | Process the DAF analysis through the edgeR package |
| process_mbzinb | Process the DAF analysis through the mbzinb package |
| process_metagenomeSeq | Process the DAF analysis through the metagenomeSeq package |
| process_RAIDA | Process the DAF analysis through the RAIDA package |
| process_voom | Process the DAF analysis through the vomm method of the limma... |
| process_wilcox | Process the DAF analysis through a wilcoxon test |
| process_ZIBseq | Process the DAF analysis through the ZIBseq package |
| QinJ_2012_metadata | Qin 2012 metadata |
| QinJ_2012_table_count | Qin 2012 table count |
| rank_features | Compare methods features rank |
| run_DAF_analysis | Run differentially abundant features analysis. |
| select_process | Select processing function to call |
| ZellerG_2014_metadata | Zeller 2014 study metadata |
| ZellerG_2014_table_count | Zeller 2014 count table |
