{ "_id": "6a1fdd3cb401979e7343852f", "Package": "KBoost", "Type": "Package", "Title": "Inference of gene regulatory networks from gene expression data", "Version": "1.21.0", "Authors@R": "c(\nperson(given = \"Luis F.\",\nfamily = \"Iglesias-Martinez\",\nrole = c(\"aut\", \"cre\"),\nemail = \"luis.iglesiasmartinez@ucd.ie\",\ncomment = c(ORCID = \"0000-0002-9110-2189\")),\nperson(given = \"Barbara\",\nfamily = \"de Kegel\",\nrole = \"aut\"),\nperson(given = \"Walter\",\nfamily = \"Kolch\",\nrole = \"aut\"))", "Description": "Reconstructing gene regulatory networks and transcription\nfactor activity is crucial to understand biological processes\nand holds potential for developing personalized treatment. Yet,\nit is still an open problem as state-of-art algorithm are often\nnot able to handle large amounts of data. Furthermore, many of\nthe present methods predict numerous false positives and are\nunable to integrate other sources of information such as\npreviously known interactions. Here we introduce KBoost, an\nalgorithm that uses kernel PCA regression, boosting and\nBayesian model averaging for fast and accurate reconstruction\nof gene regulatory networks. KBoost can also use a prior\nnetwork built on previously known transcription factor targets.\nWe have benchmarked KBoost using three different datasets\nagainst other high performing algorithms. The results show that\nour method compares favourably to other methods across\ndatasets.", "License": "GPL-2 | GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "URL": "https://github.com/Luisiglm/KBoost", "biocViews": "Network, GraphAndNetwork, Bayesian, NetworkInference,\nGeneRegulation, Transcriptomics, SystemsBiology, Transcription,\nGeneExpression, Regression, PrincipalComponent", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:11 UTC", "RemoteUrl": "https://github.com/bioc/KBoost", "RemoteRef": "HEAD", "RemoteSha": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 07:49:22 UTC", "User": "root" }, "Author": "Luis F. Iglesias-Martinez [aut, cre] (ORCID:\n),\nBarbara de Kegel [aut],\nWalter Kolch [aut]", "Maintainer": "Luis F. Iglesias-Martinez ", "MD5sum": "d4d1236089e0b2ea2b3f212fd9e73e8e", "_user": "bioc", "_type": "src", "_file": "KBoost_1.21.0.tar.gz", "_fileid": "7cddae8cf474f92f3a08872e56f744380639afe3d34a5554e62c201f82f8c694", "_filesize": 649092, "_sha256": "7cddae8cf474f92f3a08872e56f744380639afe3d34a5554e62c201f82f8c694", "_created": "2026-06-03T07:49:22.000Z", "_published": "2026-06-03T07:52:28.597Z", "_jobs": [ { "job": 79246672402, "time": 140, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7378716340" }, { "job": 79246672410, "time": 146, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7378718473" }, { "job": 79246672429, "time": 124, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7378711215" }, { "job": 79246672493, "time": 111, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7378706811" }, { "job": 79246672496, "time": 115, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7378707907" }, { "job": 79246190294, "time": 184, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7378667512" }, { "job": 79246672426, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7378701559" }, { "job": 79246672423, "time": 77, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7378695503" }, { "job": 79246672394, "time": 80, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7378696375" }, { "job": 79246672465, "time": 113, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7378708200" } ], "_bioccheck": { "error": 0, "warning": 3, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/KBoost", "_commit": { "id": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380971 }, "_maintainer": { "name": "Luis F. Iglesias-Martinez", "email": "luis.iglesiasmartinez@ucd.ie", "login": "luisiglm", "description": "I am a postdoctoral researcher in Systems Biology Ireland. My work focuses on developing machine learning approaches to study cancer. ", "uuid": 63861892, "orcid": "0000-0002-9110-2189" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "network", "graphandnetwork", "bayesian", "networkinference", "generegulation", "transcriptomics", "systemsbiology", "transcription", "geneexpression", "regression", "principalcomponent" ], "_stars": 4, "_contributors": [ { "user": "luisiglm", "count": 55, "uuid": 63861892 }, { "user": "dekegel", "count": 2, "uuid": 6524896 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 246, "source": "https://www.bioconductor.org/packages/stats/bioc/KBoost" }, "_mentions": 1, "_devurl": "https://github.com/luisiglm/kboost", "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/KBoost.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/luisiglm/kboost", "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_names", "AUPR_AUROC_matrix", "d4_mfac", "get_prior_Gerstein", "get_tfs_human", "grid_search_kboost", "irma_check", "kboost", "KBoost_human_symbol", "kernel_normal", "kernel_pc_boosting", "KPC", "net_dist_bin", "net_refine", "net_summary_bin", "RBF_K", "tab_2_matrix_D4", "write_GRN_D4" ], "_datasets": [ { "name": "D4_multi_1", "title": "Dream 4 multifactorial pertubation challenge dataset 1", "object": "D4_multi_1", "class": [ "matrix", "array" ], "fields": {}, "rows": 100, "table": true, "tojson": true }, { "name": "D4_multi_2", "title": "Dream 4 multifactorial pertubation challenge dataset 2", "object": "D4_multi_2", "class": [ "matrix", "array" ], "fields": {}, "rows": 100, "table": true, "tojson": true }, { "name": "D4_multi_3", "title": "Dream 4 multifactorial pertubation challenge dataset 3", "object": "D4_multi_3", "class": [ "matrix", "array" ], "fields": {}, "rows": 100, "table": true, "tojson": true }, { "name": "D4_multi_4", "title": "Dream 4 multifactorial pertubation challenge dataset 4", "object": "D4_multi_4", "class": [ "matrix", "array" ], "fields": {}, "rows": 100, "table": true, "tojson": true }, { "name": "D4_multi_5", "title": "Dream 4 multifactorial pertubation challenge dataset 5", "object": "D4_multi_5", "class": [ "matrix", "array" ], "fields": {}, "rows": 100, "table": true, "tojson": true }, { "name": "G_D4_multi_1", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 1", "object": "G_D4_multi_1", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3" ], "rows": 176, "table": true, "tojson": true }, { "name": "G_D4_multi_2", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 2", "object": "G_D4_multi_2", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3" ], "rows": 249, "table": true, "tojson": true }, { "name": "G_D4_multi_3", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 3", "object": "G_D4_multi_3", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3" ], "rows": 195, "table": true, "tojson": true }, { "name": "G_D4_multi_4", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 4", "object": "G_D4_multi_4", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3" ], 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This function was made to test the R implementation of the KBoost Package.", "topics": [ "AUPR_AUROC_matrix" ] }, { "page": "d4_mfac", "title": "Function to obtain the AUPR and AUROC in the DREAM4 Multifactorial Challenge.", "topics": [ "d4_mfac" ] }, { "page": "D4_multi_1", "title": "Dream 4 multifactorial pertubation challenge dataset 1", "topics": [ "D4_multi_1" ] }, { "page": "D4_multi_2", "title": "Dream 4 multifactorial pertubation challenge dataset 2", "topics": [ "D4_multi_2" ] }, { "page": "D4_multi_3", "title": "Dream 4 multifactorial pertubation challenge dataset 3", "topics": [ "D4_multi_3" ] }, { "page": "D4_multi_4", "title": "Dream 4 multifactorial pertubation challenge dataset 4", "topics": [ "D4_multi_4" ] }, { "page": "D4_multi_5", "title": "Dream 4 multifactorial pertubation challenge dataset 5", "topics": [ "D4_multi_5" ] }, { "page": "G_D4_multi_1", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 1", "topics": [ "G_D4_multi_1" ] }, { "page": "G_D4_multi_2", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 2", "topics": [ "G_D4_multi_2" ] }, { "page": "G_D4_multi_3", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 3", "topics": [ "G_D4_multi_3" ] }, { "page": "G_D4_multi_4", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 4", "topics": [ "G_D4_multi_4" ] }, { "page": "G_D4_multi_5", "title": "Gold Standard Dream 4 multifactorial pertubation challenge dataset 5", "topics": [ "G_D4_multi_5" ] }, { "page": "Gerstein_Prior_ENET_2", "title": "Gene Regulatory Network from human ChIP-Seq data in Encode", "topics": [ "Gerstein_Prior_ENET_2" ] }, { "page": "get_prior_Gerstein", "title": "Function to build a prior using a previously built Network on ChIP-Seq.", "topics": [ "get_prior_Gerstein" ] }, { "page": "get_tfs_human", "title": "Function to automatically assign Human TFs given a list of Symbols.", "topics": [ "get_tfs_human" ] }, { "page": "grid_search_kboost", "title": "Function to perform a grid search and find the hyperparameters.", "topics": [ "grid_search_kboost" ] }, { "page": "Human_TFs", "title": "Index of human genes' Symbols, Entrez and Ensembl for K-Boost Pacakge that correspond to transcription factors.", "topics": [ "Human_TFs" ] }, { "page": "irma_check", "title": "Function to produce the AUPR and AUROC Results on the IRMA datasets.", "topics": [ "irma_check" ] }, { "page": "IRMA_Gold", "title": "IRMA Gold Standard Network", "topics": [ "IRMA_Gold" ] }, { "page": "irma_off", "title": "IRMA Off Dataset", "topics": [ "irma_off" ] }, { "page": "irma_on", "title": "IRMA On Dataset", "topics": [ "irma_on" ] }, { "page": "kboost", "title": "A function to run KBoost.", "topics": [ "kboost" ] }, { "page": "KBoost_human_symbol", "title": "Function for KBoost on data from a human sample annotated with Symbol names.", "topics": [ "KBoost_human_symbol" ] }, { "page": "kernel_normal", "title": "A function to perform feature normalization in kernel space.", "topics": [ "kernel_normal" ] }, { "page": "kernel_pc_boosting", "title": "Function to perform Kernel Principal Component Boosting", "topics": [ "kernel_pc_boosting" ] }, { "page": "KPC", "title": "Function to calculate the principal components of a kernel.", "topics": [ "KPC" ] }, { "page": "net_dist_bin", "title": "Function to calculate the distance between nodes.", "topics": [ "net_dist_bin" ] }, { "page": "net_refine", "title": "Function to do a heuristic post-processing that improves accuracy. Each column is multiplied by its variance.", "topics": [ "net_refine" ] }, { "page": "net_summary_bin", "title": "Function to summarize the GRN filtered with a threshold,", "topics": [ "net_summary_bin" ] }, { "page": "RBF_K", "title": "Function to calculate the RBF Kernel of a matrix X with width g.", "topics": [ "RBF_K" ] }, { "page": "tab_2_matrix_D4", "title": "Function to produce the gold standard of the DREAM4 Multifactorial Challenge in matrix format.", "topics": [ "tab_2_matrix_D4" ] }, { "page": "write_GRN_D4", "title": "Function to write output in DREAM4 Challenge Format.", "topics": [ "write_GRN_D4" ] } ], "_readme": "https://github.com/bioc/KBoost/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "KBoost.Rmd", "filename": "KBoost.html", "title": "KBoost", "author": "Luis F. Iglesias-Martinez, Barbara De Kegel and Walter Kolch", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quickstart", "Without Prior knowledge:", "With Prior knowledge:", "With gene symbols", "Main Functions", "KBoost(X, TFs, prior_weights, g, v, ite)", "KBoost_human_symbol(X, gen_names, g, v, ite, pos_weight, neg_weight)", "AUPR_AUROC_matrix(Net, G_mat, auto_remove, TFs, upper_limit)", "d4_mfac(v, g, ite)", "get_prior_Gerstein(gen_names, TFs, pos_weight, neg_weight)", "grid_search_kboost(dataset, vs, gs, ite)", "irma_check(g, v, ite)", "net_dist_bin(GRN,TFs,thr)", "net_summary_bin(GRN,TFs,thr,a,b)", "net_refine(Net)", "write_GRN_D4(GRN,TFs, filename)", "Datasets", "DREAM 4 Multifactorial Perturbation Challenge Datasets", "D4_multi_1, D4_multi_2, D4_multi_3, D4_multi_4 and D4_multi_5", "G_D4_multi_1, G_D4_multi_2, G_D4_multi_3, G_D4_multi_4 and G_D4_multi_5", "Gerstein_Prior_ENET_2", "Human_TFs" ], "created": "2021-01-25 17:05:06", "modified": "2021-04-01 13:43:57", "commits": 2 } ], "_score": 4.748188027006201, "_indexed": true, "_nocasepkg": "kboost", "_universes": [ "bioc", "luisiglm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-03T07:51:42.000Z", "distro": "noble", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "2bcbd2ef57aac330f114fd33f310ef1155d5b8e693f1ac0e18ff75fec09db0ab", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-03T07:51:24.000Z", "distro": "noble", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "7b84360a56627e598e09a387ad18f1debb8dea8ff1bbccd95cc007e914040146", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-03T07:51:13.000Z", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "fbdf6c1563d3593f700b0e446ed939da96670e4f3a5d8fe76386ddefeb130826", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-03T07:51:14.000Z", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "35da34796f334c180a97ef09cad0447e7e5e2ee650011cfeeccbbab4c838bf3f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-06-03T07:51:16.000Z", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "c19236d7e6ca3455b7de786609598ab167e2a9cf824d81cf0fdd49981ece6fea", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-06-03T07:50:29.000Z", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "0597dad82528cbe203beb2fa3632662628c090662a9070f23a92e8941487a9f3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-06-03T07:50:35.000Z", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "617bade9453ea2948fd1664ad1bcdccf509a9284c2c75dc2c50cf211c8dfc556", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-06-03T07:51:05.000Z", "commit": "f359b85b1fef8c57a98de7bdb8c774d870d9b688", "fileid": "706617d6f01f47c0e66fcae19f28002c3e4aff91c6f13780f8bae11358be5761", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871035306" } ] }