Man pages for kimberlyroche/codaDE
What the Package Does in One 'Title Case' Line
| build_Athanasiadou_reference | Generate differential expression reference for Athanasiadou... |
| build_Barlow_reference | Generate differential expression reference for Barlow et al.... |
| build_Morton_reference | Generate differential expression reference for Morton et al.... |
| build_simulated_reference | Generate simulated differential expression for two conditions |
| calc_DA_discrepancy | Calculates the discrepancy between differential abundance... |
| calc_threshold_DA | Threshold to generate calls on differentially abundant... |
| call_DA_ALDEx2 | Evaluate differential abundance with ALDEx2 |
| call_DA_ANCOMBC | Evaluate differential abundance with ANCOM-BC |
| call_DA_DESeq2 | Evaluate differential abundance with DESeq2 (via Seurat) |
| call_DA_edgeR | Evaluate differential abundance with edgeR |
| call_DA_MAST | Evaluate differential abundance with MAST (via Seurat) |
| call_DA_NB | Evaluate differential abundance with a negative binomial GLM... |
| call_DA_scran | Evaluate differential abundance with scran |
| characterize_dataset | Generate simulated differential expression for two conditions |
| compute_sf | Compute reference-derived per-sample scale factor |
| DA_by_ALDEx2 | Wrapper for call_DA_ALDEx2 generating reference and target... |
| DA_by_ANCOMBC | Wrapper for call_DA_ANCOMBC generating reference and target... |
| DA_by_DESeq2 | Wrapper for call_DA_DESeq2 generating reference and target... |
| DA_by_edgeR | Wrapper for call_DA_edgeR generating reference and target... |
| DA_by_MAST | Wrapper for call_DA_MAST generating reference and target... |
| DA_by_NB | Wrapper for call_DA_NB generating reference and target calls |
| DA_by_scran | Wrapper for call_DA_scran generating reference and target... |
| DA_wrapper | Wrapper function for differential abundance calling |
| fit_predictive_model | Generate simulated differential expression for two conditions |
| generate_highcontrast_palette | Generate a color palette suitable for stacked bar plots given... |
| get_timestamp | Generate a current timestamp in Y-m-d H:M:S format |
| normalize_Athanasiadou | Utility function that applies the ERCC normalization code... |
| parse_Athanasiadou | Parse the Athanasiadou et al. (2021) bulk RNA-seq data |
| parse_Barlow | Parse the Barlow et al. (2020) 16S data |
| parse_ESCA | Parse the TCGA ESCA RNA-seq data |
| parse_Ferreira | Parse the Ferreira et al. (2014) zebrafish bulk RNA-seq data... |
| parse_Gruen | Parse the Gruen et al. (2014) single-cell cell line data set |
| parse_Hagai | Parse the Hagai et al. (2018) cross-species, cross-cell,... |
| parse_Hashimshony | Parse the Hashimshony et al. (2016) mouse fibroblast data set |
| parse_Kimmerling | Parse the Kimmerling et al. (2018) fibroblast data set |
| parse_Klein | Parse the Klein et al. (2015) mouse +/- LIF data set |
| parse_Monaco | Parse the Monaco et al. (2019) immune cell data set |
| parse_Morton | Parse the Morton et al. (2019) 16S data |
| parse_Muraro | Parse the Muraro et al. (2016) single-cell pancreas data set |
| parse_Owens | Parse the Owens et al. (2016) zebrafish developmental series |
| parse_Song | Parse the Song et al. (2021) nCounter data |
| parse_VieiraSilva | Parse the Vieira-Silva et al. (2019) QMP data set |
| parse_Yu | Parse the Yu et al. (2014) rat tissue bulk RNA-seq |
| plot_bipartite_graph | Generate a bipartite graph for differential... |
| plot_stacked_bars | Generate a color palette suitable for stacked bar plots given... |
| pull_features | Generate simulated differential expression for two conditions |
| resample_counts | Utility function to multinomially resample counts |
| scaled_counts_ALDEx2 | Scale counts using ALDEx2-like size factors |
| scaled_counts_DESeq2 | Scale counts using DESeq2-like size factors |
| scaled_counts_scran | Scale counts using scran-like size factors |
| simulate_sequence_counts | Simulate UMI count single-cell RNA-seq data |
| spike_in_ones | Utility function to spike-in a one-count to prevent any fully... |
| wrangle_validation_data | Compute reference-derived per-sample scale factor |
