Man pages for CogDisResLab/KRSA
KRSA: Kinome Random Sampling Analyzer
| ballModel_edges | Protein-Protein Interactions based on PhosphositePlus... |
| ballModel_nodes | Protein-Protein Interactions based on PhosphositePlus... |
| enrichr_lib_call | Runs enrichr api (single GET call for a geneset library) |
| krsa | Main KRSA function. It performs the random sampling analysis... |
| krsa_ball_model | Generates a kinase ball model using the Z score table |
| krsa_ce_output_kinases | It prepares a KRSA kinase file to be used for creedenzymatic |
| krsa_ce_output_peptides | It prepares a KRSA peptide file (log2 FC) to be used for... |
| krsa_coverage_plot | Generates a coverage plot (Percentage of total coverage of... |
| KRSA_coverage_PTK_PamChip_86402_v1 | KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping) |
| KRSA_coverage_STK_PamChip_87102_v1 | KRSA kinase coverage file for PamChip 87102 STK (v1 mapping) |
| KRSA_coverage_STK_PamChip_87102_v2 | KRSA kinase coverage file for PamChip 87102 STK (v2 mapping,... |
| krsa_curve_plot | Generates curves plots per peptide using the last cycle data |
| krsa_cv_plot | Generates CV (coefficient of variation) plot |
| krsa_enrichr | Runs enrichr analysis using a list of PamChip peptide IDs or... |
| krsa_enrichr_plot | Visualize the enrichr analysis |
| krsa_extractEndPoint | Extracts end point data (last cycle) |
| krsa_extractEndPointMaxExp | Extracts end point data at max exposure (last cycle) |
| krsa_filter_lowPeps | Filters out peptides with low signals based on the pw data... |
| krsa_filter_nonLinear | Filters out peptides with none linear signals based on the pw... |
| krsa_filter_ref_pep | Filters out ref peptides |
| krsa_get_diff | Extract differential peptides based on LFC cutoff |
| krsa_get_diff_byChip | Extract differential peptides based on LFC cutoff by... |
| krsa_group_diff | Calculates LFC based on modeled pw data and grouping |
| krsa_heatmap | Generates a heatmap based on the modeled pw data |
| krsa_heatmap_grouped | Generates a grouped heatmap |
| krsa_histogram_plot | Generates kinase histogram plots based on the KRSA function... |
| KRSA_Mapping_PTK_PamChip_86402_v1 | KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1... |
| KRSA_Mapping_STK_PamChip_87102_v1 | KRSA kinase-substrate mapping file for PamChip 87102 STK (v1... |
| krsa_qc_steps | QC pre-processing of raw data (deals with negative values,... |
| krsa_quick_filter | Filters out low signal peptides AND none linear peptides |
| krsa_read | Read crosstab format files exported from bioNavigator and... |
| krsa_reverse_krsa_plot | Generates the reverse krsa plot (to examine kinase activity) |
| krsa_sampling | Performs random sampling of peptides and mapped kinases |
| krsa_scaleModel | Fits, scales, transforms, and normalize kinome array data |
| krsa_show_peptides | Determine number of peptides inside lists |
| krsa_top_hits | Extracts top kinase hits based on a Z cutoff |
| krsa_violin_plot | Generates violin plots based on peptides signals intensities |
| krsa_violin_plot_grouped | Generates grouped violin plots based on peptides signals... |
| krsa_waterfall | Generates a waterfall figure based on the LFC table |
| krsa_zscores_plot | Generates a waterfall figure based on the Z score table |
| parse_BN_crosstabFile | Parse bionavigator crosstab files |
| ptk_pamchip_86402_mapping | CDRL Complete mapping of peptides to HGNC symbols (PTK... |
| reexports | Objects exported from other packages |
| stk_pamchip_87102_mapping | CDRL Complete mapping of peptides to HGNC symbols (STK... |
