{ "_id": "6a15705facfb0bcc41d64e0f", "Package": "KINNET", "Type": "Package", "Title": "Kinase INteraction NETwork Generation", "Version": "0.4.0.9002", "Authors@R": "c(\nperson(given = c(\"Ali\", \"Sajid\"),\nfamily = \"Imami\",\nrole = c(\"aut\", \"cre\"),\nemail = \"Ali.Sajid.Imami@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3684-3539\")),\nperson(given = \"Khaled\",\nfamily = \"Alganem\",\nrole = c(\"aut\"),\nemail = \"Khaled.Alganem@rockets.utoledo.edu\",\ncomment = c(ORCID = \"0000-0003-3234-7669\")),\nperson(given = c(\"Justin\", \"Fortune\"),\nfamily = \"Creeden\",\nrole = c(\"aut\"),\nemail = \"Justin.Creeden@rockets.utoledo.edu\",\ncomment = c(ORCID = \"0000-0003-3123-8401\")),\nperson(given = \"Alex\",\nfamily = \"Joyce\",\nrole = c(\"aut\"),\nemail = \"Alex.Joyce2@rockets.utoledo.edu\",\ncomment = c(ORCID = \"0000-0003-0303-2481\")))", "Description": "This package provides the functionality to process\nPamGene's PamChip Data Output and generate kinase interaction\nnetworks from that. This project uses a bayesian algorithm to\ngenerate bayesian networks for defining dependence\nrelationships between peptide sequences in the PamChip data. It\nthen uses a novel kinase assignment method to assign upstream\nkinases to each peptide which is then output as a graph.", "License": "GPL (>= 3) | file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "Collate": "'assign_kinases.R' 'compare_kinased_graphs.R' 'distances.R'\n'equalize_kinase_graphs.R' 'filter_peptides.R' 'make_model.R'\n'pamchip_data.R' 'pamchip_data_ptk.R' 'pamchip_data_stk.R'\n'probability_matrix.R' 'ptk_methods.R' 'render_kinased_graph.R'\n'render_reduced_kinased_graph.R' 'stk_methods.R'\n'subset_data.R' 'update_probability_matrix.R'", "Config/testthat/edition": "3", "Repository": "https://cogdisreslab.r-universe.dev", "Date/Publication": "2022-01-14 16:32:11 UTC", "RemoteUrl": "https://github.com/CogDisResLab/KINNET", "RemoteRef": "HEAD", "RemoteSha": "8c901f74fee88662aa6630dbe536ba08e7a7af54", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 10:01:43 UTC", "User": "root" }, "Author": "Ali Sajid Imami [aut, cre] (ORCID:\n),\nKhaled Alganem [aut] (ORCID: ),\nJustin Fortune Creeden [aut] (ORCID:\n),\nAlex Joyce [aut] (ORCID: )", "Maintainer": "Ali Sajid Imami ", "MD5sum": "b15a09f6130fec45f3635cd4d180c07f", "_user": "cogdisreslab", "_type": "src", "_file": "KINNET_0.4.0.9002.tar.gz", "_fileid": "e4e767da4be05eca1d129742a61b79fd348fa1f0cbbb9f43bba0966a708527a6", "_filesize": 568668, "_sha256": "e4e767da4be05eca1d129742a61b79fd348fa1f0cbbb9f43bba0966a708527a6", "_created": "2026-05-26T10:01:43.000Z", "_published": "2026-05-26T10:05:19.594Z", "_distro": "noble", "_jobs": [ { "job": 77851297644, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7214241675" }, { "job": 77851297645, "time": 145, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7214242604" }, { "job": 77851297626, "time": 165, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7214238623" }, { "job": 77851297636, "time": 183, "config": "macos-release-arm64", "r": 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"time": 1642177931 }, "_maintainer": { "name": "Ali Sajid Imami", "email": "ali.sajid.imami@gmail.com", "login": "alisajid", "orcid": "0000-0003-3684-3539", "twitter": "@doctor_no", "description": "", "uuid": 395482 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "bnlearn", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "Rgraphviz", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "effectsize", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cogdisreslab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "alisajid", "count": 70, "uuid": 395482 }, { "user": "a-w-j", "count": 2, "uuid": 75330469 } ], "_userbio": { "uuid": 83421213, "type": "organization", "name": "Cognitive Disorders Research Lab" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/KINNET" }, "_devurl": "https://github.com/cogdisreslab/kinnet", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/KINNET.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "assign_kinases", "assign_kinases_guided", "classes", "compare_kinased_graphs", "equalize_kinase_graphs", "exp_data", "filter_peptides", "fit_standardized", "kinnet_hamming", "kinnet_normalized_hamming", "kinnet_normalized_shd", "kinnet_shd", "make_model", "PamchipData_PTK", "PamchipData_STK", "peptides", "pheno_data", "render_kinased_graph", "render_reduced_kinased_graph", "subset_data", "update_probability_matrix" ], "_help": [ { "page": "assign_kinases", "title": "Assign kinases, given a network and a chip type", "topics": [ "assign_kinases" ] }, { "page": "assign_kinases_guided", "title": "Assign kinases, given a network and a chip type and additional essential kinases", "topics": [ "assign_kinases_guided" ] }, { "page": "candidate_kinases", "title": "Generate Candidate Kinases Based On Links", "topics": [ "candidate_kinases" ] }, { "page": "compare_kinased_graphs", "title": "Compare two kinased graphhs", "topics": [ "compare_kinased_graphs" ] }, { "page": "equalize_kinase_graphs", "title": "Equalize the nodesets of two kinased graphs", "topics": [ "equalize_kinase_graphs" ] }, { "page": "filter_peptides", "title": "Return a list of significant peptides", "topics": [ "filter_peptides" ] }, { "page": "fit_standardized", "title": "Do a standardized fit of expression data from a single peptide's activity", "topics": [ "fit_standardized" ] }, { "page": "get_intersections", "title": "Generate Intersections between kinases", "topics": [ "get_intersections" ] }, { "page": "kinnet_hamming", "title": "Calculate the Hamming Distance between two kinased graphs", "topics": [ "kinnet_hamming" ] }, { "page": "kinnet_normalized_hamming", "title": "Calculate Normalized Hamming Distance", "topics": [ "kinnet_normalized_hamming" ] }, { "page": "kinnet_normalized_shd", "title": "Calculate Normalized Structural Hamming Distance", "topics": [ "kinnet_normalized_shd" ] }, { "page": "kinnet_shd", "title": "Calculate the Structural Hamming Distance between two kinased graphs", "topics": [ "kinnet_shd" ] }, { "page": "make_model", "title": "Generate a bayes net model", "topics": [ "make_model" ] }, { "page": "PamchipData_PTK", "title": "Process a file into a usable structure", "topics": [ "PamchipData_PTK" ] }, { "page": "PamchipData_STK", "title": "Process a file into a usable structure", "topics": [ "PamchipData_STK" ] }, { "page": "PamchipData-class", "title": "The Pamchip Data Superclass", "topics": [ "PamchipData-class" ] }, { "page": "PamchipData-PTK-class", "title": "A representation of the PamChip PTK Data", "topics": [ "PamchipData-PTK-class" ] }, { "page": "PamchipData-STK-class", "title": "A representation of the PamChip STK Data", "topics": [ "PamchipData-STK-class" ] }, { "page": "ptk_probability_matrix_gene", "title": "PTK Peptide to Kinase Probability Matrix for Gene Identifiers", "topics": [ "ptk_probability_matrix_gene" ] }, { "page": "ptk_probability_matrix_kinase", "title": "PTK Peptide to Kinase Probability Matrix for Kinase Identifiers", "topics": [ "ptk_probability_matrix_kinase" ] }, { "page": "render_kinased_graph", "title": "Generate a kianse graph", "topics": [ "render_kinased_graph" ] }, { "page": "render_reduced_kinased_graph", "title": "Generate a reduced kianse graph", "topics": [ "render_reduced_kinased_graph" ] }, { "page": "safely_add_node", "title": "Add a node safely to a bn object", "topics": [ "safely_add_node" ] }, { "page": "stk_accessors", "title": "STK Data Accessor Functions", "topics": [ "classes", "classes,PamchipData-STK-method", "exp_data", "exp_data,PamchipData-STK-method", "peptides", "peptides,PamchipData-STK-method", "pheno_data", "pheno_data,PamchipData-STK-method", "stk_accessors" ] }, { "page": "stk_probability_matrix_gene", "title": "STK Peptide to Kinase Probability Matrix for Gene Identifiers", "topics": [ "stk_probability_matrix_gene" ] }, { "page": "stk_probability_matrix_kinase", "title": "STK Peptide to Kinase Probability Matrix for Kinase Identifiers", "topics": [ "stk_probability_matrix_kinase" ] }, { "page": "subset_data", "title": "Subset The Kinome Data", "topics": [ "subset_data" ] }, { "page": "update_probability_matrix", "title": "Calculated Updated Probabilities of each peptide/kinase pair", "topics": [ "update_probability_matrix" ] } ], "_readme": "https://github.com/CogDisResLab/KINNET/raw/HEAD/README.md", "_rundeps": [ "bayestestR", "BiocGenerics", "bit", "bit64", "bnlearn", "cli", "clipr", "cpp11", "crayon", "datawizard", "dplyr", "effectsize", "generics", "glue", "graph", "hms", "insight", "lifecycle", "magrittr", "parameters", "performance", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "readr", "Rgraphviz", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_score": 2, "_indexed": true, "_nocasepkg": "kinnet", "_universes": [ "cogdisreslab", "alisajid" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.0.9002", "date": "2026-05-26T10:03:49.000Z", "distro": "noble", "commit": "8c901f74fee88662aa6630dbe536ba08e7a7af54", "fileid": "9c9f03e3f2275a89e14493827ea516da7cc2c4f35850fe5e8ef9903b12023ea4", "status": "success", "check": "WARNING", "buildurl": 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