| add_names | Function to add names to network for the user. |
| AUPR_AUROC_matrix | Function to calculate the AUROC and AUPR of a known network.... |
| d4_mfac | Function to obtain the AUPR and AUROC in the DREAM4... |
| D4_multi_1 | Dream 4 multifactorial pertubation challenge dataset 1 |
| D4_multi_2 | Dream 4 multifactorial pertubation challenge dataset 2 |
| D4_multi_3 | Dream 4 multifactorial pertubation challenge dataset 3 |
| D4_multi_4 | Dream 4 multifactorial pertubation challenge dataset 4 |
| D4_multi_5 | Dream 4 multifactorial pertubation challenge dataset 5 |
| G_D4_multi_1 | Gold Standard Dream 4 multifactorial pertubation challenge... |
| G_D4_multi_2 | Gold Standard Dream 4 multifactorial pertubation challenge... |
| G_D4_multi_3 | Gold Standard Dream 4 multifactorial pertubation challenge... |
| G_D4_multi_4 | Gold Standard Dream 4 multifactorial pertubation challenge... |
| G_D4_multi_5 | Gold Standard Dream 4 multifactorial pertubation challenge... |
| Gerstein_Prior_ENET_2 | Gene Regulatory Network from human ChIP-Seq data in Encode |
| get_prior_Gerstein | Function to build a prior using a previously built Network on... |
| get_tfs_human | Function to automatically assign Human TFs given a list of... |
| grid_search_kboost | Function to perform a grid search and find the... |
| Human_TFs | Index of human genes' Symbols, Entrez and Ensembl for K-Boost... |
| irma_check | Function to produce the AUPR and AUROC Results on the IRMA... |
| IRMA_Gold | IRMA Gold Standard Network |
| irma_off | IRMA Off Dataset |
| irma_on | IRMA On Dataset |
| kboost | A function to run KBoost. |
| KBoost_human_symbol | Function for KBoost on data from a human sample annotated... |
| kernel_normal | A function to perform feature normalization in kernel space. |
| kernel_pc_boosting | Function to perform Kernel Principal Component Boosting |
| KPC | Function to calculate the principal components of a kernel. |
| net_dist_bin | Function to calculate the distance between nodes. |
| net_refine | Function to do a heuristic post-processing that improves... |
| net_summary_bin | Function to summarize the GRN filtered with a threshold, |
| RBF_K | Function to calculate the RBF Kernel of a matrix X with width... |
| tab_2_matrix_D4 | Function to produce the gold standard of the DREAM4... |
| write_GRN_D4 | Function to write output in DREAM4 Challenge Format. |
