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"HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "NCIH1781_LUNG", "NCIH3255_LUNG", "EFO21_OVARY", "PECAPJ15_UPPER_AERODIGESTIVE_TRACT", "SKUT1_SOFT_TISSUE", "NCIH1355_LUNG", "SNU899_UPPER_AERODIGESTIVE_TRACT", "F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "CL11_LARGE_INTESTINE", "BECKER_CENTRAL_NERVOUS_SYSTEM", "SNU478_BILIARY_TRACT", "L1236_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "KMBC2_URINARY_TRACT", "BEN_LUNG", "OCIAML2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "CAPAN1_PANCREAS", "HCC95_LUNG", "CW2_LARGE_INTESTINE", "SW837_LARGE_INTESTINE", "PATU8902_PANCREAS", "BT474_BREAST", "SCC15_UPPER_AERODIGESTIVE_TRACT", "NCIH661_LUNG", "MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "SNB19_CENTRAL_NERVOUS_SYSTEM", "CADOES1_BONE", "SW1088_CENTRAL_NERVOUS_SYSTEM", "JHH2_LIVER", "FTC238_THYROID", "OCUM1_STOMACH", "PANC0813_PANCREAS", "SNU245_BILIARY_TRACT", "IALM_LUNG", "GCIY_STOMACH", "CAKI2_KIDNEY", "DKMG_CENTRAL_NERVOUS_SYSTEM", "GSU_STOMACH", "NCO2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "TT2609C02_THYROID", "YD15_SALIVARY_GLAND", "MELHO_SKIN", "CAOV3_OVARY", "ISHIKAWAHERAKLIO02ER_ENDOMETRIUM", "MDAMB361_BREAST", "JMSU1_URINARY_TRACT", "HS229T_LUNG", "DETROIT562_UPPER_AERODIGESTIVE_TRACT", "X8MGBA_CENTRAL_NERVOUS_SYSTEM", "FUOV1_OVARY", "CORL279_LUNG", "MIAPACA2_PANCREAS", "KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "SKMEL2_SKIN", "HT1376_URINARY_TRACT", "NCIH2347_LUNG", "X42MGBA_CENTRAL_NERVOUS_SYSTEM", "NCIH1105_LUNG", "KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "DMS53_LUNG", "KPNRTBM1_AUTONOMIC_GANGLIA", "MELJUSO_SKIN", "HCC1395_BREAST", "KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "SNU398_LIVER", "TE5_OESOPHAGUS", "SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "TUHR10TKB_KIDNEY", "SW1271_LUNG", "TE8_OESOPHAGUS", "HS294T_SKIN", "ABC1_LUNG", "RPMI7951_SKIN", "NIHOVCAR3_OVARY", "BHT101_THYROID", "HCC1937_BREAST", "SHP77_LUNG", "SNU119_OVARY", "NCIH441_LUNG", "SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "SNU407_LARGE_INTESTINE", "NCIH2122_LUNG", "MONOMAC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "H4_CENTRAL_NERVOUS_SYSTEM", "ML1_THYROID", "JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "ME1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "COV434_OVARY", "SNU475_LIVER", "X639V_URINARY_TRACT", "RKO_LARGE_INTESTINE", "SKMEL31_SKIN", "GCT_SOFT_TISSUE", "KYSE140_OESOPHAGUS", "NCIH1792_LUNG", "LAMA84_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "GDM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "GP2D_LARGE_INTESTINE", "OVISE_OVARY", "HEC59_ENDOMETRIUM", "REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "NCIH2030_LUNG", "NCIH1581_LUNG", "COV362_OVARY", "SKNFI_AUTONOMIC_GANGLIA", "HCC44_LUNG", "P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "RT4_URINARY_TRACT", "MFE319_ENDOMETRIUM", "SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "SNU601_STOMACH", "SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "TCCPAN2_PANCREAS", "HS172T_URINARY_TRACT", "COLO783_SKIN", "ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "NCIH2023_LUNG", "KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "U251MG_CENTRAL_NERVOUS_SYSTEM", "X786O_KIDNEY", "ES2_OVARY", "SF295_CENTRAL_NERVOUS_SYSTEM", "DMS454_LUNG", "HCC202_BREAST", "KNS62_LUNG", "MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "TE441T_SOFT_TISSUE", "NCIH1963_LUNG", "WM88_SKIN", "KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "HUH6_LIVER", "NCIH2172_LUNG", "DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "NCIH1755_LUNG", "NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "NCIH1563_LUNG", "GRM_SKIN", "SUIT2_PANCREAS", "KYSE150_OESOPHAGUS", "GMS10_CENTRAL_NERVOUS_SYSTEM", "SW900_LUNG", "OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "X59M_OVARY", "A2058_SKIN", "BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "G361_SKIN", "OVTOKO_OVARY", "PC3_PROSTATE", "SNU489_CENTRAL_NERVOUS_SYSTEM", "IGR37_SKIN", "CAL54_KIDNEY", "SW1463_LARGE_INTESTINE", "TGBC11TKB_STOMACH", "NCIH446_LUNG", "KMRC2_KIDNEY", "HS746T_STOMACH", "SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE", "HSC4_UPPER_AERODIGESTIVE_TRACT", "LK2_LUNG", "SNU761_LIVER", "T24_URINARY_TRACT", "HCC1419_BREAST" ], "rows": 1000, "table": true, "tojson": true }, { "name": "Mitochondrial_genes", "title": "List of known mitochondrial genes", "object": "Mitochondrial_genes", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "CCLE_samples", "title": "Clinical information for CCLE data", "topics": [ "CCLE_samples" ] }, { "page": "CCLE_small", "title": "Subset of expression levels of CCLE data", "topics": [ "CCLE_small" ] }, { "page": "CorScoreCalc", "title": "Calculate correlation score", "topics": [ "CorScoreCalc" ] }, { "page": "CVEval", "title": "Method for the calculation of a correlation vector", "topics": [ "CVEval" ] }, { "page": "CVPlot", "title": "Make correlation vector plot", "topics": [ "CVPlot" ] }, { "page": "FindSeed", "title": "Find highly correlated seed of samples for gene expression matrix", "topics": [ "FindSeed" ] }, { "page": "GOEnrichmentAnalysis", "title": "Calculate gene set enrichment of correlation vector using Mann-Whitney test", "topics": [ "GOEnrichmentAnalysis" ] }, { "page": "HclustGenesHiCor", "title": "Find the most highly correlated genes using hierarchical clustering", "topics": [ "HclustGenesHiCor" ] }, { "page": "MCbiclust", "title": "MCbiclust: Massively Correlated biclustering", "topics": [ "MCbiclust-package", "MCbiclust" ] }, { "page": "Mitochondrial_genes", "title": "List of known mitochondrial genes", "topics": [ "Mitochondrial_genes" ] }, { "page": "PC1VecFun", "title": "Calculate PC1 vector of found pattern", "topics": [ "PC1VecFun" ] }, { "page": "PointScoreCalc", "title": "Calculate PointScore", "topics": [ "PointScoreCalc" ] }, { "page": "SampleSort", "title": "Methods for ordering samples", "topics": [ "MultiSampleSortPrep", "SampleSort" ] }, { "page": "SilhouetteClustGroups", "title": "Slihouette validation of correlation vector clusters", "topics": [ "SilhouetteClustGroups" ] }, { "page": "ThresholdBic", "title": "Methods for defining a bicluster", "topics": [ "ForkClassifier", "PC1Align", "ThresholdBic" ] } ], "_readme": "https://github.com/bioc/MCbiclust/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "checkmate", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "digest", "doParallel", "dplyr", "dynamicTreeCut", "evaluate", "farver", "fastcluster", "fastmap", "fontawesome", "forcats", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GGally", "ggplot2", "ggstats", "glue", "GO.db", "gridExtra", "gtable", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "memoise", "mime", "nnet", "openssl", "org.Hs.eg.db", "patchwork", "pillar", "pkgconfig", "png", "preprocessCore", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "rpart", "RSQLite", "rstudioapi", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "WGCNA", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "MCbiclust_vignette.Rmd", "filename": "MCbiclust_vignette.html", "title": "Introduction to MCbiclust", "author": "Robert Bentham", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting started", "Example of a single run", "Loading Cancer Cell Line Encyclopedia (CCLE) and MitoCarta data sets", "Finding a bicluster seed", "Selecting highly correlated genes", "Calculate the correlation vector", "Gene Set Enrichment", "Sample ordering", "PCA", "Thresholding the bicluster and aligning PC1", "Alternative to PCA", "Plotting the forks", "Comparing results with sample data", "CCLE sample data", "Dealing with multiple runs", "Identifying samples related to a known bicluster in different data sets", "PointScore", "ssGSEA", "Session Info", "References" ], "created": "2016-08-17 15:33:46", "modified": "2024-02-11 17:09:47", "commits": 27 } ], "_score": 4, "_indexed": true, "_nocasepkg": "mcbiclust", "_universes": [ "bioc", "rbentham" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-06-04T11:23:59.000Z", "distro": "noble", "commit": "9d5df1fd29d4272fe386f97bbc99ba1632003ca8", "fileid": "5d43e85ebff36f545a167683d2a2028eea3c51b37fb670f0ccfb51b511ad86e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26948235352" }, { "r": "4.6.0", "os": "linux", "version": "1.37.0", "date": "2026-06-04T11:23:52.000Z", "distro": "noble", "commit": "9d5df1fd29d4272fe386f97bbc99ba1632003ca8", "fileid": 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