From 2682a5c62e770d737bfaaaea6d8aefe9f62e016a Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 2 Jul 2025 04:10:14 +0000 Subject: [PATCH] chore(deps): update dependency font-awesome to v5.15.4 --- docs/dev/LICENSE-text.html | 2 +- docs/dev/LICENSE.html | 2 +- docs/dev/authors.html | 2 +- docs/dev/index.html | 4 ++-- docs/dev/reference/KRSA_Mapping_PTK_PamChip_86402_v1.html | 2 +- docs/dev/reference/KRSA_Mapping_STK_PamChip_87102_v1.html | 2 +- docs/dev/reference/KRSA_coverage_PTK_PamChip_86402_v1.html | 2 +- docs/dev/reference/KRSA_coverage_STK_PamChip_87102_v1.html | 2 +- docs/dev/reference/KRSA_coverage_STK_PamChip_87102_v2.html | 2 +- docs/dev/reference/ballModel_edges.html | 2 +- docs/dev/reference/ballModel_nodes.html | 2 +- docs/dev/reference/enrichr_lib_call.html | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/krsa.html | 2 +- docs/dev/reference/krsa_ball_model.html | 2 +- docs/dev/reference/krsa_ce_output_kinases.html | 2 +- docs/dev/reference/krsa_ce_output_peptides.html | 2 +- docs/dev/reference/krsa_coverage_plot.html | 2 +- docs/dev/reference/krsa_curve_plot.html | 2 +- docs/dev/reference/krsa_cv_plot.html | 2 +- docs/dev/reference/krsa_enrichr.html | 2 +- docs/dev/reference/krsa_enrichr_plot.html | 2 +- docs/dev/reference/krsa_extractEndPoint.html | 2 +- docs/dev/reference/krsa_extractEndPointMaxExp.html | 2 +- docs/dev/reference/krsa_filter_lowPeps.html | 2 +- docs/dev/reference/krsa_filter_nonLinear.html | 2 +- docs/dev/reference/krsa_filter_ref_pep.html | 2 +- docs/dev/reference/krsa_get_diff.html | 2 +- docs/dev/reference/krsa_get_diff_byChip.html | 2 +- docs/dev/reference/krsa_group_diff.html | 2 +- docs/dev/reference/krsa_heatmap.html | 2 +- docs/dev/reference/krsa_heatmap_grouped.html | 2 +- docs/dev/reference/krsa_histogram_plot.html | 2 +- docs/dev/reference/krsa_qc_steps.html | 2 +- docs/dev/reference/krsa_quick_filter.html | 2 +- docs/dev/reference/krsa_read.html | 2 +- docs/dev/reference/krsa_reverse_krsa_plot.html | 2 +- docs/dev/reference/krsa_sampling.html | 2 +- docs/dev/reference/krsa_scaleModel.html | 2 +- docs/dev/reference/krsa_show_peptides.html | 2 +- docs/dev/reference/krsa_top_hits.html | 2 +- docs/dev/reference/krsa_violin_plot.html | 2 +- docs/dev/reference/krsa_violin_plot_grouped.html | 2 +- docs/dev/reference/krsa_waterfall.html | 2 +- docs/dev/reference/krsa_zscores_plot.html | 2 +- docs/dev/reference/parse_BN_crosstabFile.html | 2 +- docs/dev/reference/ptk_pamchip_86402_mapping.html | 2 +- docs/dev/reference/reexports.html | 2 +- docs/dev/reference/stk_pamchip_87102_mapping.html | 2 +- 49 files changed, 50 insertions(+), 50 deletions(-) diff --git a/docs/dev/LICENSE-text.html b/docs/dev/LICENSE-text.html index 45f10c6..60831f3 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..31bfbdb 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..7c84bf5 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..89b8075 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -15,8 +15,8 @@ - - + + 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..42c4793 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..70bfdd3 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..e0ddaf1 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..fbb4071 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..4eb6919 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..f3f1c44 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..64e4b8c 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..e7d0838 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..90a2374 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..a742fe2 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..97b7ed0 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..f0e4c7e 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..c20c3e5 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..1ade127 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..092b02a 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..9b1a70c 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..75a2471 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..349aab5 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..0755877 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..db5ef68 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..28b2f44 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..76d75cb 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..f8a12c5 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..7ee5425 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..bef2f7f 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..4b0e257 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..ee49f42 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..00d8f8e 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..2f369fd 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..0ef8ccd 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..9e651f9 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..4ea2f9f 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