Daniele Pittari

Thank you for your enquiry. To compute the prediction values, the function `evaluate_target_prediction_strict `calls `classification_evaluation_continuous_pred` using the response and prediction vectors as inputs. Inside `classification_evaluation_continuous_pred` you will find all the...

Thank you for your interest in NicheNet. We have not defined a specific cutoff of AUPR/AUPR corrected because these values can show high variability among different datasets. I would stress...

Thank you for your interest in our model. The `ligand_tf_matrix` is the output of the personalized page rank (PPR) algorithm. We used it to estimate signal propagation from ligands to...

Dear user, is the package `ComplexHeatmap` currently installed and functional on your system?

Dear user, in order to help you with your requests, I'll require additional information: 1. How did you generate your list of target genes? Are those putative target genes of...

Dear Paria, In this case, I suggest utilising an over-representation analysis approach (enrichment procedures based on Fisher's exact test / hypergeometric distribution). This kind of approach requires the definition of...

Dear Joshua, thank you for using our tool. I believe the approach you would like to utilize resembles the classical data-driven exploration for the inference of sender-receiver behaviours, such as...

Dear user, we observed that nominal AUPR values can vary across different datasets. This is why establishing a hard cutoff is not a procedure we suggest. If the known ligand-target...

@APuchkina The true positives used for the AUPR computation are the DEGs, and the negative ones are the background genes. The AUPR scores are associated with how the ligands explain...

Dear Dmitry, Thank you for your interest in NicheNet and apologies for the delay in our reply. >My main goal is to retrieve the activated receptors. I wonder what the...