{ "_id": "6a1035f1acfb0bcc41c99d86", "Package": "KRSA", "Title": "KRSA: Kinome Random Sampling Analyzer", "Version": "1.99.354", "Authors@R": "c(person(c(\"Ali\", \"Sajid\"), \"Imami\", , \"Ali.Sajid.Imami@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3684-3539\")),\nperson(c(\"Khaled\"), \"Alganem\", ,\"khaled.a.alganem@gmail.com\" ,role = \"aut\", comment = c(ORCID = \"0000-0003-4419-3708\")))", "Description": "The goal of this package is to analyze the PamChip data\nand identify the changes in the active kinome. The package can\npreprocess the PamChip data output from BioNavigator and use\nRandom Sampling and Permutation Analysis to identify upstream\nkinases. Additionally, this package provides a set of useful\nvisualizations for the PamChip data.", "License": "MIT + file LICENSE", "URL": "https://github.com/CogDisResLab/KRSA,\nhttps://cogdisreslab.github.io/KRSA/", "Encoding": "UTF-8", "BugReports": "https://github.com/CogDisResLab/KRSA/issues", "biocViews": "Software", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/testthat/parallel": "TRUE", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "LazyData": "true", "Repository": "https://cogdisreslab.r-universe.dev", "Date/Publication": "2026-01-12 03:56:09 UTC", "RemoteUrl": "https://github.com/CogDisResLab/KRSA", "RemoteRef": "HEAD", "RemoteSha": "ce1209d9e10beb03d37b9107e776493dcd943002", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 07:04:12 UTC", "User": "root" }, "Author": "Ali Sajid Imami [aut, cre] (ORCID:\n),\nKhaled Alganem [aut] (ORCID: )", "Maintainer": "Ali Sajid Imami ", "MD5sum": "12496b57ab825b078a35049a8052c31c", "_user": "cogdisreslab", "_type": "src", "_file": "KRSA_1.99.354.tar.gz", "_fileid": "0d69a072d0a2180024d30636606d0dba22c392e16a9829a106df0adcc7633a6b", "_filesize": 3637492, "_sha256": "0d69a072d0a2180024d30636606d0dba22c392e16a9829a106df0adcc7633a6b", "_created": "2026-05-12T07:04:12.000Z", "_published": "2026-05-22T10:54:41.338Z", "_distro": "noble", "_jobs": [ { "job": 77365486232, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6937794035" }, { "job": 77365486272, "time": 160, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6937790223" }, { "job": 77365486097, "time": 104, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6937773746" }, { "job": 77365485930, "time": 99, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6937771931" }, { "job": 77365485492, "time": 244, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "6937743432" }, { "job": 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Imami", "email": "ali.sajid.imami@gmail.com", "login": "alisajid", "orcid": "0000-0003-3684-3539", "twitter": "@doctor_no", "uuid": 395482 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "magrittr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "EnvStats", "role": "Imports" }, { "package": "broom", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ggsignif", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "gt", "role": "Suggests" }, { "package": "furrr", "role": "Suggests" }, { "package": "biocthis", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" }, { "package": "gganimate", "role": "Suggests" } ], "_owner": "cogdisreslab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-27", "n": 108 }, { "week": "2025-33", "n": 4 }, { "week": "2025-35", "n": 3 }, { "week": "2025-52", "n": 2 }, { "week": "2026-03", "n": 1 } ], "_tags": [ { "name": "1.99.13", "date": "2025-08-25" }, { "name": "v1.99.354", "date": "2025-08-25" } ], "_topics": [ "kinase", "phosphatases", "pamchip", "kinome", "random\nsampling", "permutation analysis" ], "_stars": 4, "_contributors": [ { "user": "alisajid", "count": 125, "uuid": 395482 }, { "user": "kalganem", "count": 56, "uuid": 37287792 } ], "_userbio": { "uuid": 83421213, "type": "organization", "name": "Cognitive Disorders Research Lab" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/KRSA" }, "_devurl": "https://github.com/cogdisreslab/krsa", "_pkgdown": "https://cogdisreslab.github.io/KRSA/", "_searchresults": 72, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/KRSA.html", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "%>%", "enrichr_lib_call", "krsa", "krsa_ball_model", "krsa_ce_output_kinases", "krsa_ce_output_peptides", "krsa_coverage_plot", "krsa_curve_plot", "krsa_cv_plot", "krsa_enrichr", "krsa_enrichr_plot", "krsa_extractEndPoint", "krsa_extractEndPointMaxExp", "krsa_filter_lowPeps", "krsa_filter_nonLinear", "krsa_filter_ref_pep", "krsa_get_diff", "krsa_get_diff_byChip", "krsa_group_diff", "krsa_heatmap", "krsa_heatmap_grouped", "krsa_histogram_plot", "krsa_qc_steps", "krsa_quick_filter", "krsa_read", "krsa_reverse_krsa_plot", "krsa_sampling", "krsa_scaleModel", "krsa_show_peptides", "krsa_top_hits", "krsa_violin_plot", "krsa_violin_plot_grouped", "krsa_waterfall", "krsa_zscores_plot", "parse_BN_crosstabFile" ], "_datasets": [ { "name": "ballModel_edges", "title": "Protein-Protein Interactions based on PhosphositePlus database", "object": "ballModel_edges", "class": [ "data.frame" ], "fields": [ "Source", "Target" ], "rows": 592, "table": true, "tojson": true }, { "name": "ballModel_nodes", "title": "Protein-Protein Interactions based on PhosphositePlus database", "object": "ballModel_nodes", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "FinName", "count" ], "rows": 179, "table": true, "tojson": true }, { "name": "KRSA_coverage_PTK_PamChip_86402_v1", "title": "KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping)", "object": "KRSA_coverage_PTK_PamChip_86402_v1", "class": [ "data.frame" ], "fields": [ "Kin", "Substrates" ], "rows": 1278, "table": true, "tojson": true }, { "name": "KRSA_coverage_STK_PamChip_87102_v1", "title": "KRSA kinase coverage file for PamChip 87102 STK (v1 mapping)", "object": "KRSA_coverage_STK_PamChip_87102_v1", "class": [ "data.frame" ], "fields": [ "Kin", "Substrates" ], "rows": 2423, "table": true, "tojson": true }, { "name": "KRSA_coverage_STK_PamChip_87102_v2", "title": "KRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase)", "object": "KRSA_coverage_STK_PamChip_87102_v2", "class": [ "data.frame" ], "fields": [ "Kin", "Substrates" ], "rows": 2422, "table": true, "tojson": true }, { "name": "KRSA_layout_PTK_PamChip_86402_v1", "title": "", "object": "KRSA_layout_PTK_PamChip_86402_v1", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "Row Col ID Sequence Tyr SpotConc UniprotAccession Description Xoff Yoff" ], "rows": 204, "table": true, "tojson": true }, { "name": "KRSA_layout_STK_PamChip_87102_v1", "title": "", "object": "KRSA_layout_STK_PamChip_87102_v1", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "Row Col ID Sequence Ser Thr SpotConc UniprotAccession Description Xoff Yoff" ], "rows": 152, "table": true, "tojson": true }, { "name": "KRSA_Mapping_PTK_PamChip_86402_v1", "title": "KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping)", "object": "KRSA_Mapping_PTK_PamChip_86402_v1", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "Substrates", "Kinases" ], "rows": 193, "table": true, "tojson": true }, { "name": "KRSA_Mapping_STK_PamChip_87102_v1", "title": "KRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping)", "object": "KRSA_Mapping_STK_PamChip_87102_v1", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "Substrates", "Kinases" ], "rows": 141, "table": true, "tojson": true }, { "name": "KRSA_uka_mapping_PTK_PamChip_86402_v1", "title": "", "object": "KRSA_uka_mapping_PTK_PamChip_86402_v1", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "ID", "PepProtein_UniprotName", "PepProtein_UniprotID", "PepProtein_Residue", "PepProtein_PhosLink", "PepProtein_SeqHomology", "Kinase_UniprotID", "Kinase_UniprotName", "Database", "Analysis", "exists" ], "rows": 1438, "table": true, "tojson": true }, { "name": "KRSA_uka_mapping_STK_PamChip_87102_v1", "title": "", "object": "KRSA_uka_mapping_STK_PamChip_87102_v1", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "ID", "PepProtein_UniprotName", "PepProtein_UniprotID", "PepProtein_Residue", "PepProtein_PhosLink", "PepProtein_SeqHomology", "Kinase_UniprotID", "Kinase_UniprotName", "Database", "Analysis", "exists" ], "rows": 2106, "table": true, "tojson": true }, { "name": "ptk_pamchip_86402_mapping", "title": "CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)", "object": "ptk_pamchip_86402_mapping", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ID", "HGNC" ], "rows": 193, "table": true, "tojson": true }, { "name": "stk_pamchip_87102_mapping", "title": "CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)", "object": "stk_pamchip_87102_mapping", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ID", "HGNC" ], "rows": 141, "table": true, "tojson": true } ], "_help": [ { "page": "ballModel_edges", "title": "Protein-Protein Interactions based on PhosphositePlus database", "topics": [ "ballModel_edges" ] }, { "page": "ballModel_nodes", "title": "Protein-Protein Interactions based on PhosphositePlus database", "topics": [ "ballModel_nodes" ] }, { "page": "enrichr_lib_call", "title": "Runs enrichr api (single GET call for a geneset library)", "concept": [ "helper functions" ], "topics": [ "enrichr_lib_call" ] }, { "page": "krsa", "title": "Main KRSA function. It performs the random sampling analysis and generates a Z score table and a count matrix", "concept": [ "core functions" ], "topics": [ "krsa" ] }, { "page": "krsa_ball_model", "title": "Generates a kinase ball model using the Z score table", "concept": [ "plots" ], "topics": [ "krsa_ball_model" ] }, { "page": "krsa_ce_output_kinases", "title": "It prepares a KRSA kinase file to be used for creedenzymatic", "concept": [ "helper functions" ], "topics": [ "krsa_ce_output_kinases" ] }, { "page": "krsa_ce_output_peptides", "title": "It prepares a KRSA peptide file (log2 FC) to be used for creedenzymatic", "concept": [ "helper functions" ], "topics": [ "krsa_ce_output_peptides" ] }, { "page": "krsa_coverage_plot", "title": "Generates a coverage plot (Percentage of total coverage of kinases on chip)", "concept": [ "plots" ], "topics": [ "krsa_coverage_plot" ] }, { "page": "KRSA_coverage_PTK_PamChip_86402_v1", "title": "KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping)", "topics": [ "KRSA_coverage_PTK_PamChip_86402_v1" ] }, { "page": "KRSA_coverage_STK_PamChip_87102_v1", "title": "KRSA kinase coverage file for PamChip 87102 STK (v1 mapping)", "topics": [ "KRSA_coverage_STK_PamChip_87102_v1" ] }, { "page": "KRSA_coverage_STK_PamChip_87102_v2", "title": "KRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase)", "topics": [ "KRSA_coverage_STK_PamChip_87102_v2" ] }, { "page": "krsa_curve_plot", "title": "Generates curves plots per peptide using the last cycle data", "concept": [ "plots" ], "topics": [ "krsa_curve_plot" ] }, { "page": "krsa_cv_plot", "title": "Generates CV (coefficient of variation) plot", "concept": [ "plots" ], "topics": [ "krsa_cv_plot" ] }, { "page": "krsa_enrichr", "title": "Runs enrichr analysis using a list of PamChip peptide IDs or genes", "concept": [ "helper functions" ], "topics": [ "krsa_enrichr" ] }, { "page": "krsa_enrichr_plot", "title": "Visualize the enrichr analysis", "concept": [ "plotting functions" ], "topics": [ "krsa_enrichr_plot" ] }, { "page": "krsa_extractEndPoint", "title": "Extracts end point data (last cycle)", "concept": [ "helper functions" ], "topics": [ "krsa_extractEndPoint" ] }, { "page": "krsa_extractEndPointMaxExp", "title": "Extracts end point data at max exposure (last cycle)", "concept": [ "helper functions" ], "topics": [ "krsa_extractEndPointMaxExp" ] }, { "page": "krsa_filter_lowPeps", "title": "Filters out peptides with low signals based on the pw data (max exposure)", "concept": [ "QC functions" ], "topics": [ "krsa_filter_lowPeps" ] }, { "page": "krsa_filter_nonLinear", "title": "Filters out peptides with none linear signals based on the pw data", "concept": [ "QC functions" ], "topics": [ "krsa_filter_nonLinear" ] }, { "page": "krsa_filter_ref_pep", "title": "Filters out ref peptides", "concept": [ "QC functions" ], "topics": [ "krsa_filter_ref_pep" ] }, { "page": "krsa_get_diff", "title": "Extract differential peptides based on LFC cutoff", "concept": [ "helper functions" ], "topics": [ "krsa_get_diff" ] }, { "page": "krsa_get_diff_byChip", "title": "Extract differential peptides based on LFC cutoff by chip/barcode", "concept": [ "helper functions" ], "topics": [ "krsa_get_diff_byChip" ] }, { "page": "krsa_group_diff", "title": "Calculates LFC based on modeled pw data and grouping", "concept": [ "core functions" ], "topics": [ "krsa_group_diff" ] }, { "page": "krsa_heatmap", "title": "Generates a heatmap based on the modeled pw data", "concept": [ "plots" ], "topics": [ "krsa_heatmap" ] }, { "page": "krsa_heatmap_grouped", "title": "Generates a grouped heatmap", "concept": [ "plots" ], "topics": [ "krsa_heatmap_grouped" ] }, { "page": "krsa_histogram_plot", "title": "Generates kinase histogram plots based on the KRSA function output", "concept": [ "plots" ], "topics": [ "krsa_histogram_plot" ] }, { "page": "KRSA_Mapping_PTK_PamChip_86402_v1", "title": "KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping)", "topics": [ "KRSA_Mapping_PTK_PamChip_86402_v1" ] }, { "page": "KRSA_Mapping_STK_PamChip_87102_v1", "title": "KRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping)", "topics": [ "KRSA_Mapping_STK_PamChip_87102_v1" ] }, { "page": "krsa_qc_steps", "title": "QC pre-processing of raw data (deals with negative values, and adjust signal saturation values)", "concept": [ "QC functions" ], "topics": [ "krsa_qc_steps" ] }, { "page": "krsa_quick_filter", "title": "Filters out low signal peptides AND none linear peptides", "concept": [ "core functions" ], "topics": [ "krsa_quick_filter" ] }, { "page": "krsa_read", "title": "Read crosstab format files exported from bioNavigator and tidy them", "concept": [ "core functions" ], "topics": [ "krsa_read" ] }, { "page": "krsa_reverse_krsa_plot", "title": "Generates the reverse krsa plot (to examine kinase activity)", "concept": [ "plots" ], "topics": [ "krsa_reverse_krsa_plot" ] }, { "page": "krsa_sampling", "title": "Performs random sampling of peptides and mapped kinases", "concept": [ "helper functions" ], "topics": [ "krsa_sampling" ] }, { "page": "krsa_scaleModel", "title": "Fits, scales, transforms, and normalize kinome array data", "concept": [ "core functions" ], "topics": [ "krsa_scaleModel" ] }, { "page": "krsa_show_peptides", "title": "Determine number of peptides inside lists", "concept": [ "helper functions" ], "topics": [ "krsa_show_peptides" ] }, { "page": "krsa_top_hits", "title": "Extracts top kinase hits based on a Z cutoff", "concept": [ "helper functions" ], "topics": [ "krsa_top_hits" ] }, { "page": "krsa_violin_plot", "title": "Generates violin plots based on peptides signals intensities", "concept": [ "plots" ], "topics": [ "krsa_violin_plot" ] }, { "page": "krsa_violin_plot_grouped", "title": "Generates grouped violin plots based on peptides signals intensities with t tests options", "concept": [ "plots" ], "topics": [ "krsa_violin_plot_grouped" ] }, { "page": "krsa_waterfall", "title": "Generates a waterfall figure based on the LFC table", "concept": [ "plots" ], "topics": [ "krsa_waterfall" ] }, { "page": "krsa_zscores_plot", "title": "Generates a waterfall figure based on the Z score table", "concept": [ "plots" ], "topics": [ "krsa_zscores_plot" ] }, { "page": "parse_BN_crosstabFile", "title": "Parse bionavigator crosstab files", "topics": [ "parse_BN_crosstabFile" ] }, { "page": "ptk_pamchip_86402_mapping", "title": "CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)", "topics": [ "ptk_pamchip_86402_mapping" ] }, { "page": "stk_pamchip_87102_mapping", "title": "CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)", "topics": [ "stk_pamchip_87102_mapping" ] } ], "_pkglogo": "https://github.com/CogDisResLab/KRSA/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/CogDisResLab/KRSA/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "bit", "bit64", "broom", "cli", "clipr", "cpp11", "crayon", "curl", "dplyr", "EnvStats", 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