Man pages for lusystemsbio/NetAct
NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity
| Activity_heatmap | Plotting TF gene expresion & activity heatmap |
| allNet | Compile a GSDB to a matrix with 2 columns |
| applyDPI | Apply data processing inequality |
| cal_activity | The core function to compute the activity profile of an TF |
| calculateMI | Calculate mutual information |
| DEG_Analysis_Micro | Helper Function For DEG Analysis of microArray Data (for a... |
| filterDB | Filtered gene set database based on minimum sizes |
| getAdjacencyMat | Obtain the adjacency matrix from a matrix of tf-target... |
| GSEA_permut_R | Compute ES scores for Gene Set Enrichment Analysis (GSEA)... |
| GSEA_permut_R_revised | Compute ES scores for Gene Set Enrichment Analysis (GSEA)... |
| GSEA_proc_R | Gene Set Enrichment Analysis (GSEA) with a new permutation... |
| GSEA_proc_RC | Gene Set Enrichment Analysis (GSEA) with a new permutation... |
| GSEA_score | Compute the enrichment score (ES) from Gene Set Enrichment... |
| hDB | Human transcription factor target regulatory database |
| Hill | Hill function for the gene weight |
| mDB | Mouse transcription factor target regulatory database |
| MicroDegs | Helper Function For DEG Analysis of microArray Data (for all... |
| plot_network | Plotting gene network |
| Preprocess_counts | RNA-seq data pre processing |
| rem_data | Remove Non-informative genes |
| Reselect_TFs | Reselecting TFs using gene set enrichement analysis (GSEA)... |
| RNAseqDegs_DESeq | Helper Function For DEG Analysis of RNA-seq Data using DESeq |
| RNAseqDegs_limma | Helper Function For DEG Analysis of RNA-seq Data using limma... |
| row_norm | Row normalization (standardization) |
| TF_Activity | Inference of TF activity |
| TF_Filter | Generate network |
| TF_Filter_addgene | Generate network (an extension of TF_Filter) |
| TF_GSEA | A unified Gene Set Enrichment Analysis (GSEA) function for... |
| TF_Selection | Identifying enriched TFs using Gene Set Enrichment Analysis... |
| toCPM | convert to log10 (CPM) measurement in the RNA-Seq matrix |
