diff --git a/docs/dev/LICENSE-text.html b/docs/dev/LICENSE-text.html index 45f10c6..051b02a 100644 --- a/docs/dev/LICENSE-text.html +++ b/docs/dev/LICENSE-text.html @@ -1,5 +1,5 @@ -License • KRSALicense • KRSA diff --git a/docs/dev/LICENSE.html b/docs/dev/LICENSE.html index 6d4fb47..f00673b 100644 --- a/docs/dev/LICENSE.html +++ b/docs/dev/LICENSE.html @@ -1,5 +1,5 @@ -MIT License • KRSAMIT License • KRSA diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 4b33196..5ba7577 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • KRSAAuthors and Citation • KRSA diff --git a/docs/dev/index.html b/docs/dev/index.html index ca8d202..a44cbc0 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -17,7 +17,7 @@ - + diff --git a/docs/dev/reference/KRSA_Mapping_PTK_PamChip_86402_v1.html b/docs/dev/reference/KRSA_Mapping_PTK_PamChip_86402_v1.html index a5a355b..21e8889 100644 --- a/docs/dev/reference/KRSA_Mapping_PTK_PamChip_86402_v1.html +++ b/docs/dev/reference/KRSA_Mapping_PTK_PamChip_86402_v1.html @@ -1,6 +1,6 @@ KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping) — KRSA_Mapping_PTK_PamChip_86402_v1 • KRSAKRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping) — KRSA_Mapping_PTK_PamChip_86402_v1 • KRSAKRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping) — KRSA_Mapping_STK_PamChip_87102_v1 • KRSAKRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping) — KRSA_Mapping_STK_PamChip_87102_v1 • KRSAKRSA kinase coverage file for PamChip 86402 PTK (v1 mapping) — KRSA_coverage_PTK_PamChip_86402_v1 • KRSAKRSA kinase coverage file for PamChip 86402 PTK (v1 mapping) — KRSA_coverage_PTK_PamChip_86402_v1 • KRSAKRSA kinase coverage file for PamChip 87102 STK (v1 mapping) — KRSA_coverage_STK_PamChip_87102_v1 • KRSAKRSA kinase coverage file for PamChip 87102 STK (v1 mapping) — KRSA_coverage_STK_PamChip_87102_v1 • KRSAKRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase) — KRSA_coverage_STK_PamChip_87102_v2 • KRSAKRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase) — KRSA_coverage_STK_PamChip_87102_v2 • KRSAProtein-Protein Interactions based on PhosphositePlus database — ballModel_edges • KRSAProtein-Protein Interactions based on PhosphositePlus database — ballModel_edges • KRSAProtein-Protein Interactions based on PhosphositePlus database — ballModel_nodes • KRSAProtein-Protein Interactions based on PhosphositePlus database — ballModel_nodes • KRSARuns enrichr api (single GET call for a geneset library) — enrichr_lib_call • KRSARuns enrichr api (single GET call for a geneset library) — enrichr_lib_call • KRSAFunction reference • KRSAFunction reference • KRSA diff --git a/docs/dev/reference/krsa.html b/docs/dev/reference/krsa.html index ef138c7..08038be 100644 --- a/docs/dev/reference/krsa.html +++ b/docs/dev/reference/krsa.html @@ -1,5 +1,5 @@ -Main KRSA function. It performs the random sampling analysis and generates a Z score table and a count matrix — krsa • KRSAMain KRSA function. It performs the random sampling analysis and generates a Z score table and a count matrix — krsa • KRSA diff --git a/docs/dev/reference/krsa_ball_model.html b/docs/dev/reference/krsa_ball_model.html index 814f73d..8eaaa60 100644 --- a/docs/dev/reference/krsa_ball_model.html +++ b/docs/dev/reference/krsa_ball_model.html @@ -1,5 +1,5 @@ -Generates a kinase ball model using the Z score table — krsa_ball_model • KRSAGenerates a kinase ball model using the Z score table — krsa_ball_model • KRSA diff --git a/docs/dev/reference/krsa_ce_output_kinases.html b/docs/dev/reference/krsa_ce_output_kinases.html index 7923a60..2a83a06 100644 --- a/docs/dev/reference/krsa_ce_output_kinases.html +++ b/docs/dev/reference/krsa_ce_output_kinases.html @@ -1,5 +1,5 @@ -It prepares a KRSA kinase file to be used for creedenzymatic — krsa_ce_output_kinases • KRSAIt prepares a KRSA kinase file to be used for creedenzymatic — krsa_ce_output_kinases • KRSA diff --git a/docs/dev/reference/krsa_ce_output_peptides.html b/docs/dev/reference/krsa_ce_output_peptides.html index 893ba06..dadffb9 100644 --- a/docs/dev/reference/krsa_ce_output_peptides.html +++ b/docs/dev/reference/krsa_ce_output_peptides.html @@ -1,5 +1,5 @@ -It prepares a KRSA peptide file (log2 FC) to be used for creedenzymatic — krsa_ce_output_peptides • KRSAIt prepares a KRSA peptide file (log2 FC) to be used for creedenzymatic — krsa_ce_output_peptides • KRSA diff --git a/docs/dev/reference/krsa_coverage_plot.html b/docs/dev/reference/krsa_coverage_plot.html index f4c7758..d684999 100644 --- a/docs/dev/reference/krsa_coverage_plot.html +++ b/docs/dev/reference/krsa_coverage_plot.html @@ -1,5 +1,5 @@ -Generates a coverage plot (Percentage of total coverage of kinases on chip) — krsa_coverage_plot • KRSAGenerates a coverage plot (Percentage of total coverage of kinases on chip) — krsa_coverage_plot • KRSA diff --git a/docs/dev/reference/krsa_curve_plot.html b/docs/dev/reference/krsa_curve_plot.html index 64e36b2..de22164 100644 --- a/docs/dev/reference/krsa_curve_plot.html +++ b/docs/dev/reference/krsa_curve_plot.html @@ -1,5 +1,5 @@ -Generates curves plots per peptide using the last cycle data — krsa_curve_plot • KRSAGenerates curves plots per peptide using the last cycle data — krsa_curve_plot • KRSA diff --git a/docs/dev/reference/krsa_cv_plot.html b/docs/dev/reference/krsa_cv_plot.html index 18443b5..4745098 100644 --- a/docs/dev/reference/krsa_cv_plot.html +++ b/docs/dev/reference/krsa_cv_plot.html @@ -1,5 +1,5 @@ -Generates CV (coefficient of variation) plot — krsa_cv_plot • KRSAGenerates CV (coefficient of variation) plot — krsa_cv_plot • KRSA diff --git a/docs/dev/reference/krsa_enrichr.html b/docs/dev/reference/krsa_enrichr.html index e73138a..0ef5309 100644 --- a/docs/dev/reference/krsa_enrichr.html +++ b/docs/dev/reference/krsa_enrichr.html @@ -1,5 +1,5 @@ -Runs enrichr analysis using a list of PamChip peptide IDs or genes — krsa_enrichr • KRSARuns enrichr analysis using a list of PamChip peptide IDs or genes — krsa_enrichr • KRSA diff --git a/docs/dev/reference/krsa_enrichr_plot.html b/docs/dev/reference/krsa_enrichr_plot.html index 9543bcc..6d26315 100644 --- a/docs/dev/reference/krsa_enrichr_plot.html +++ b/docs/dev/reference/krsa_enrichr_plot.html @@ -1,5 +1,5 @@ -Visualize the enrichr analysis — krsa_enrichr_plot • KRSAVisualize the enrichr analysis — krsa_enrichr_plot • KRSA diff --git a/docs/dev/reference/krsa_extractEndPoint.html b/docs/dev/reference/krsa_extractEndPoint.html index 1f4807f..5cd5f59 100644 --- a/docs/dev/reference/krsa_extractEndPoint.html +++ b/docs/dev/reference/krsa_extractEndPoint.html @@ -1,6 +1,6 @@ Extracts end point data (last cycle) — krsa_extractEndPoint • KRSAExtracts end point data (last cycle) — krsa_extractEndPoint • KRSAExtracts end point data at max exposure (last cycle) — krsa_extractEndPointMaxExp • KRSAExtracts end point data at max exposure (last cycle) — krsa_extractEndPointMaxExp • KRSAFilters out peptides with low signals based on the pw data (max exposure) — krsa_filter_lowPeps • KRSAFilters out peptides with low signals based on the pw data (max exposure) — krsa_filter_lowPeps • KRSA diff --git a/docs/dev/reference/krsa_filter_nonLinear.html b/docs/dev/reference/krsa_filter_nonLinear.html index d1f2a67..16e39bc 100644 --- a/docs/dev/reference/krsa_filter_nonLinear.html +++ b/docs/dev/reference/krsa_filter_nonLinear.html @@ -1,5 +1,5 @@ -Filters out peptides with none linear signals based on the pw data — krsa_filter_nonLinear • KRSAFilters out peptides with none linear signals based on the pw data — krsa_filter_nonLinear • KRSA diff --git a/docs/dev/reference/krsa_filter_ref_pep.html b/docs/dev/reference/krsa_filter_ref_pep.html index 045b489..bbc6698 100644 --- a/docs/dev/reference/krsa_filter_ref_pep.html +++ b/docs/dev/reference/krsa_filter_ref_pep.html @@ -1,5 +1,5 @@ -Filters out ref peptides — krsa_filter_ref_pep • KRSAFilters out ref peptides — krsa_filter_ref_pep • KRSA diff --git a/docs/dev/reference/krsa_get_diff.html b/docs/dev/reference/krsa_get_diff.html index 27c0aea..f384d13 100644 --- a/docs/dev/reference/krsa_get_diff.html +++ b/docs/dev/reference/krsa_get_diff.html @@ -1,5 +1,5 @@ -Extract differential peptides based on LFC cutoff — krsa_get_diff • KRSAExtract differential peptides based on LFC cutoff — krsa_get_diff • KRSA diff --git a/docs/dev/reference/krsa_get_diff_byChip.html b/docs/dev/reference/krsa_get_diff_byChip.html index e2b9732..82c7813 100644 --- a/docs/dev/reference/krsa_get_diff_byChip.html +++ b/docs/dev/reference/krsa_get_diff_byChip.html @@ -1,5 +1,5 @@ -Extract differential peptides based on LFC cutoff by chip/barcode — krsa_get_diff_byChip • KRSAExtract differential peptides based on LFC cutoff by chip/barcode — krsa_get_diff_byChip • KRSA diff --git a/docs/dev/reference/krsa_group_diff.html b/docs/dev/reference/krsa_group_diff.html index daf8a0d..a0966b7 100644 --- a/docs/dev/reference/krsa_group_diff.html +++ b/docs/dev/reference/krsa_group_diff.html @@ -1,5 +1,5 @@ -Calculates LFC based on modeled pw data and grouping — krsa_group_diff • KRSACalculates LFC based on modeled pw data and grouping — krsa_group_diff • KRSA diff --git a/docs/dev/reference/krsa_heatmap.html b/docs/dev/reference/krsa_heatmap.html index f633af3..5e370c8 100644 --- a/docs/dev/reference/krsa_heatmap.html +++ b/docs/dev/reference/krsa_heatmap.html @@ -1,5 +1,5 @@ -Generates a heatmap based on the modeled pw data — krsa_heatmap • KRSAGenerates a heatmap based on the modeled pw data — krsa_heatmap • KRSA diff --git a/docs/dev/reference/krsa_heatmap_grouped.html b/docs/dev/reference/krsa_heatmap_grouped.html index 1f0bb04..7f7b181 100644 --- a/docs/dev/reference/krsa_heatmap_grouped.html +++ b/docs/dev/reference/krsa_heatmap_grouped.html @@ -1,5 +1,5 @@ -Generates a grouped heatmap — krsa_heatmap_grouped • KRSAGenerates a grouped heatmap — krsa_heatmap_grouped • KRSA diff --git a/docs/dev/reference/krsa_histogram_plot.html b/docs/dev/reference/krsa_histogram_plot.html index 5b527c5..eeb20a7 100644 --- a/docs/dev/reference/krsa_histogram_plot.html +++ b/docs/dev/reference/krsa_histogram_plot.html @@ -1,5 +1,5 @@ -Generates kinase histogram plots based on the KRSA function output — krsa_histogram_plot • KRSAGenerates kinase histogram plots based on the KRSA function output — krsa_histogram_plot • KRSA diff --git a/docs/dev/reference/krsa_qc_steps.html b/docs/dev/reference/krsa_qc_steps.html index 9f2895a..dfab8a6 100644 --- a/docs/dev/reference/krsa_qc_steps.html +++ b/docs/dev/reference/krsa_qc_steps.html @@ -1,5 +1,5 @@ -QC pre-processing of raw data (deals with negative values, and adjust signal saturation values) — krsa_qc_steps • KRSAQC pre-processing of raw data (deals with negative values, and adjust signal saturation values) — krsa_qc_steps • KRSA diff --git a/docs/dev/reference/krsa_quick_filter.html b/docs/dev/reference/krsa_quick_filter.html index eed66c8..eb98f58 100644 --- a/docs/dev/reference/krsa_quick_filter.html +++ b/docs/dev/reference/krsa_quick_filter.html @@ -1,5 +1,5 @@ -Filters out low signal peptides AND none linear peptides — krsa_quick_filter • KRSAFilters out low signal peptides AND none linear peptides — krsa_quick_filter • KRSA diff --git a/docs/dev/reference/krsa_read.html b/docs/dev/reference/krsa_read.html index 5a321f3..27de9b1 100644 --- a/docs/dev/reference/krsa_read.html +++ b/docs/dev/reference/krsa_read.html @@ -1,5 +1,5 @@ -Read crosstab format files exported from bioNavigator and tidy them — krsa_read • KRSARead crosstab format files exported from bioNavigator and tidy them — krsa_read • KRSA diff --git a/docs/dev/reference/krsa_reverse_krsa_plot.html b/docs/dev/reference/krsa_reverse_krsa_plot.html index 9238186..94c4ec0 100644 --- a/docs/dev/reference/krsa_reverse_krsa_plot.html +++ b/docs/dev/reference/krsa_reverse_krsa_plot.html @@ -1,5 +1,5 @@ -Generates the reverse krsa plot (to examine kinase activity) — krsa_reverse_krsa_plot • KRSAGenerates the reverse krsa plot (to examine kinase activity) — krsa_reverse_krsa_plot • KRSA diff --git a/docs/dev/reference/krsa_sampling.html b/docs/dev/reference/krsa_sampling.html index d517902..1459c1b 100644 --- a/docs/dev/reference/krsa_sampling.html +++ b/docs/dev/reference/krsa_sampling.html @@ -1,5 +1,5 @@ -Performs random sampling of peptides and mapped kinases — krsa_sampling • KRSAPerforms random sampling of peptides and mapped kinases — krsa_sampling • KRSA diff --git a/docs/dev/reference/krsa_scaleModel.html b/docs/dev/reference/krsa_scaleModel.html index 6a10d4b..0217d11 100644 --- a/docs/dev/reference/krsa_scaleModel.html +++ b/docs/dev/reference/krsa_scaleModel.html @@ -1,5 +1,5 @@ -Fits, scales, transforms, and normalize kinome array data — krsa_scaleModel • KRSAFits, scales, transforms, and normalize kinome array data — krsa_scaleModel • KRSA diff --git a/docs/dev/reference/krsa_show_peptides.html b/docs/dev/reference/krsa_show_peptides.html index 4a72542..396e9c6 100644 --- a/docs/dev/reference/krsa_show_peptides.html +++ b/docs/dev/reference/krsa_show_peptides.html @@ -1,5 +1,5 @@ -Determine number of peptides inside lists — krsa_show_peptides • KRSADetermine number of peptides inside lists — krsa_show_peptides • KRSA diff --git a/docs/dev/reference/krsa_top_hits.html b/docs/dev/reference/krsa_top_hits.html index b2e9302..c5e540d 100644 --- a/docs/dev/reference/krsa_top_hits.html +++ b/docs/dev/reference/krsa_top_hits.html @@ -1,5 +1,5 @@ -Extracts top kinase hits based on a Z cutoff — krsa_top_hits • KRSAExtracts top kinase hits based on a Z cutoff — krsa_top_hits • KRSA diff --git a/docs/dev/reference/krsa_violin_plot.html b/docs/dev/reference/krsa_violin_plot.html index 90f4d48..8ee8cb1 100644 --- a/docs/dev/reference/krsa_violin_plot.html +++ b/docs/dev/reference/krsa_violin_plot.html @@ -1,5 +1,5 @@ -Generates violin plots based on peptides signals intensities — krsa_violin_plot • KRSAGenerates violin plots based on peptides signals intensities — krsa_violin_plot • KRSA diff --git a/docs/dev/reference/krsa_violin_plot_grouped.html b/docs/dev/reference/krsa_violin_plot_grouped.html index aeb8a71..e5e24cd 100644 --- a/docs/dev/reference/krsa_violin_plot_grouped.html +++ b/docs/dev/reference/krsa_violin_plot_grouped.html @@ -1,5 +1,5 @@ -Generates grouped violin plots based on peptides signals intensities with t tests options — krsa_violin_plot_grouped • KRSAGenerates grouped violin plots based on peptides signals intensities with t tests options — krsa_violin_plot_grouped • KRSA diff --git a/docs/dev/reference/krsa_waterfall.html b/docs/dev/reference/krsa_waterfall.html index 4d674fc..c5dd31f 100644 --- a/docs/dev/reference/krsa_waterfall.html +++ b/docs/dev/reference/krsa_waterfall.html @@ -1,5 +1,5 @@ -Generates a waterfall figure based on the LFC table — krsa_waterfall • KRSAGenerates a waterfall figure based on the LFC table — krsa_waterfall • KRSA diff --git a/docs/dev/reference/krsa_zscores_plot.html b/docs/dev/reference/krsa_zscores_plot.html index 49a88f8..90ffcde 100644 --- a/docs/dev/reference/krsa_zscores_plot.html +++ b/docs/dev/reference/krsa_zscores_plot.html @@ -1,5 +1,5 @@ -Generates a waterfall figure based on the Z score table — krsa_zscores_plot • KRSAGenerates a waterfall figure based on the Z score table — krsa_zscores_plot • KRSA diff --git a/docs/dev/reference/parse_BN_crosstabFile.html b/docs/dev/reference/parse_BN_crosstabFile.html index 2a29f17..d3cfe18 100644 --- a/docs/dev/reference/parse_BN_crosstabFile.html +++ b/docs/dev/reference/parse_BN_crosstabFile.html @@ -1,6 +1,6 @@ Parse bionavigator crosstab files — parse_BN_crosstabFile • KRSAParse bionavigator crosstab files — parse_BN_crosstabFile • KRSACDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402) — ptk_pamchip_86402_mapping • KRSACDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402) — ptk_pamchip_86402_mapping • KRSAObjects exported from other packages — reexports • KRSACDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102) — stk_pamchip_87102_mapping • KRSACDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102) — stk_pamchip_87102_mapping • KRSA