Man pages for saezlab/decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics data
| check_corr | Check correlation (colinearity) |
| convert_f_defaults | Rename columns and add defaults values if column not present |
| decouple | Evaluate multiple statistics with same input data |
| decoupleR-package | decoupleR: decoupleR: Ensemble of computational methods to... |
| dot-decoupler_mat_format | DecoupleR mat format |
| dot-decoupler_network_format | DecoupleR network format |
| dot-fit_preprocessing | Pre-processing for methods that fit networks. |
| extract_sets | Extract sets |
| filt_minsize | Filter sources with minsize targets |
| get_collectri | CollecTRI gene regulatory network. Wrapper to access... |
| get_dorothea | DoRothEA gene regulatory network. |
| get_ksn_omnipath | OmniPath kinase-substrate network |
| get_profile_of | Complete a data frame with missing combinations of data |
| get_progeny | Pathway RespOnsive GENes for activity inference (PROGENy). |
| get_resource | Wrapper to access resources inside Omnipath. This wrapper... |
| get_toy_data | Generate a toy 'mat' and 'network'. |
| intersect_regulons | Intersect network target features with input matrix. |
| pipe | Pipe operator |
| pivot_wider_profile | Pivot a data frame to wider and convert it to matrix |
| randomize_matrix | Randomize matrix |
| rename_net | Rename network |
| run_aucell | AUCell |
| run_consensus | Consensus score between methods |
| run_fgsea | Fast Gene Set Enrichment Analysis (FGSEA) |
| run_gsva | Gene Set Variation Analysis (GSVA) |
| run_mdt | Multivariate Decision Trees (MDT) |
| run_mlm | Multivariate Linear Model (MLM) |
| run_ora | Over Representation Analysis (ORA) |
| run_udt | Univariate Decision Tree (UDT) |
| run_ulm | Univariate Linear Model (ULM) |
| run_viper | Virtual Inference of Protein-activity by Enriched Regulon... |
| run_wmean | Weighted Mean (WMEAN) |
| run_wsum | Weighted Sum (WSUM) |
| run_zscore | z-score |
| show_methods | Show methods |
| show_resources | Shows available resources in Omnipath. For more information... |
| tidyeval | Tidy eval helpers |
