Man pages for saschajung/Intercom
Reconstruction of Functional Cell-Cell Communication Networks
| Background_signaling_interactome | Background signaling interactome |
| bool.data | Booleanize gene expression data |
| compatability_score | Calculating activation probabilities |
| comp_score_tf | Calculating compatibility scores |
| Data_preprocessing | Input Data to Markov Chain |
| dummy.var | Dummy variable |
| gene.coexp | Compute Co-expression Between Genes |
| get.cons.tfs | Get conserved TFs |
| get.gene.expr | Get Gene Expression Subset |
| high_probability_intermediates | Obtain high probability intermediates |
| HUMAN_Background_signaling_interactome | Intracellular signaling interactions of human genes |
| HUMAN_dummy.var | Dummy variable (Human) |
| HUMAN_intermediates | Intermediate signaling molecules (Human) |
| HUMAN_Ligands | Secreted ligands (Human) |
| HUMAN_LR | Ligand-receptor interactions (Human) |
| HUMAN_non_interface_TFs | Non-interface TFs (Human) |
| HUMAN_Receptors | Receptors (Human) |
| HUMAN_tf.db | Database of human TFs |
| HUMAN_tfs | Transcription factors (Human) |
| HUMAN_TF_TF_interactions | TF-TF-interactions (Human) |
| integrate_sig_TF | Integrate Signaling and Transcriptonal Regulation |
| InterCom | Reconstructs functional cell-cell communication networks |
| intermediates | Intermediate signaling molecules |
| Ligands | Ligands |
| LR | Ligand receptor interactions |
| Markov_chain_stationary_distribution | Obtain Stationary Distribution of Markov Chain |
| MOUSE_Background_signaling_interactome | Intracellular signaling interactions of mouse genes |
| MOUSE_dummy.var | Dummy variable (Mouse) |
| MOUSE_intermediates | Intermediate signaling molecules (Mouse) |
| MOUSE_Ligands | Secreted ligands (Mouse) |
| MOUSE_LR | Ligand-receptor interactions (Mouse) |
| MOUSE_non_interface_TFs | Non-interface TFs (Mouse) |
| MOUSE_Receptors | Receptors (Mouse) |
| MOUSE_tf.db | Database of mouse TFs |
| MOUSE_tfs | Transcription factors (Mouse) |
| MOUSE_TF_TF_interactions | TF-TF-interactions (Mouse) |
| non_interface_TFs | Non-interface TFs |
| path.prob.sum | Calculating significance of receptor-TF paths |
| product_path_weight | Calculating path weights |
| Receptors | Receptors |
| reproduceNetworks | Reconstructs Pancreas networks for 7 and 9 Wpc |
| scoringFun | Scoring ligand-receptor interactions |
| SigHotSpotter_pipeline | General Pipeline Call to SigHotSpotter |
| spcal_path_weight | Calculating compatibility scores |
| tf.db | TF database |
| tfs | TFs |
| TF_TF_interactions | TF-TF interactions |
| up_down_tfs | Classify non-interface TFs as up or down regulated |
| weight_probability | Calculating the weight probability |
