reformat_db.RdFormat the package database
reformat_db(db, version = NULL)A data frame returned from available.packages or installed.packages.
Version of the database, a self-defined text.
It reformats the data frame of the package database into a pkg_db class object.
A pkg_db class object. There are the following methods:
pkg_db$get_meta(package,field=NULL)field can take values in "Package", "Version" and "Repository".
pkg_db$get_dependency_table(package)Get the dependency table.
pkg_db$get_rev_dependency_table(package)Get the reverse dependency table.
pkg_db$package_dependencies(package,recursive=FALSE,reverse=FALSE,which="strong",simplify=FALSE)All the arguments are the same as in package_dependencies. Argument simplify controls whether to return a data frame or a simplied vector.
# \dontrun{
db = available.packages()
db2 = reformat_db(db)
#> prepare dependency table...
#> prepare reverse dependency table...
# a pkg_db object generated on 2021-10-28 can be loaded by load_pkg_db()
db2 = load_pkg_db(online = FALSE)
db2
#> A package database of 22392 packages.
#> - 18901 CRAN / 3491 Bioconductor / 0 other packages.
db2$get_meta("ComplexHeatmap")
#> Package Version Repository
#> ComplexHeatmap ComplexHeatmap 2.14.0 Bioconductor
db2$get_dependency_table("ComplexHeatmap")
#> package dependency dep_fields
#> [1,] "ComplexHeatmap" "methods" "Depends"
#> [2,] "ComplexHeatmap" "grid" "Depends"
#> [3,] "ComplexHeatmap" "graphics" "Depends"
#> [4,] "ComplexHeatmap" "stats" "Depends"
#> [5,] "ComplexHeatmap" "grDevices" "Depends"
#> [6,] "ComplexHeatmap" "circlize" "Imports"
#> [7,] "ComplexHeatmap" "GetoptLong" "Imports"
#> [8,] "ComplexHeatmap" "colorspace" "Imports"
#> [9,] "ComplexHeatmap" "clue" "Imports"
#> [10,] "ComplexHeatmap" "RColorBrewer" "Imports"
#> [11,] "ComplexHeatmap" "GlobalOptions" "Imports"
#> [12,] "ComplexHeatmap" "png" "Imports"
#> [13,] "ComplexHeatmap" "digest" "Imports"
#> [14,] "ComplexHeatmap" "IRanges" "Imports"
#> [15,] "ComplexHeatmap" "matrixStats" "Imports"
#> [16,] "ComplexHeatmap" "foreach" "Imports"
#> [17,] "ComplexHeatmap" "doParallel" "Imports"
#> [18,] "ComplexHeatmap" "codetools" "Imports"
#> [19,] "ComplexHeatmap" "testthat" "Suggests"
#> [20,] "ComplexHeatmap" "knitr" "Suggests"
#> [21,] "ComplexHeatmap" "markdown" "Suggests"
#> [22,] "ComplexHeatmap" "dendsort" "Suggests"
#> [23,] "ComplexHeatmap" "jpeg" "Suggests"
#> [24,] "ComplexHeatmap" "tiff" "Suggests"
#> [25,] "ComplexHeatmap" "fastcluster" "Suggests"
#> [26,] "ComplexHeatmap" "EnrichedHeatmap" "Suggests"
#> [27,] "ComplexHeatmap" "dendextend" "Suggests"
#> [28,] "ComplexHeatmap" "grImport" "Suggests"
#> [29,] "ComplexHeatmap" "grImport2" "Suggests"
#> [30,] "ComplexHeatmap" "glue" "Suggests"
#> [31,] "ComplexHeatmap" "GenomicRanges" "Suggests"
#> [32,] "ComplexHeatmap" "gridtext" "Suggests"
#> [33,] "ComplexHeatmap" "pheatmap" "Suggests"
#> [34,] "ComplexHeatmap" "gridGraphics" "Suggests"
#> [35,] "ComplexHeatmap" "gplots" "Suggests"
#> [36,] "ComplexHeatmap" "rmarkdown" "Suggests"
#> [37,] "ComplexHeatmap" "Cairo" "Suggests"
db2$get_rev_dependency_table("ComplexHeatmap")
#> package dependency dep_fields
#> [1,] "CIARA" "ComplexHeatmap" "Suggests"
#> [2,] "CNVScope" "ComplexHeatmap" "Suggests"
#> [3,] "IOHanalyzer" "ComplexHeatmap" "Suggests"
#> [4,] "IntLIM" "ComplexHeatmap" "Imports"
#> [5,] "MKomics" "ComplexHeatmap" "Imports"
#> [6,] "MOSS" "ComplexHeatmap" "Suggests"
#> [7,] "MitoHEAR" "ComplexHeatmap" "Imports"
#> [8,] "PALMO" "ComplexHeatmap" "Imports"
#> [9,] "RNAseqQC" "ComplexHeatmap" "Imports"
#> [10,] "RVA" "ComplexHeatmap" "Imports"
#> [11,] "SCpubr" "ComplexHeatmap" "Suggests"
#> [12,] "armada" "ComplexHeatmap" "Imports"
#> [13,] "bulkAnalyseR" "ComplexHeatmap" "Imports"
#> [14,] "circlize" "ComplexHeatmap" "Suggests"
#> [15,] "conos" "ComplexHeatmap" "Imports"
#> [16,] "countToFPKM" "ComplexHeatmap" "Depends"
#> [17,] "eclust" "ComplexHeatmap" "Suggests"
#> [18,] "grandR" "ComplexHeatmap" "Suggests"
#> [19,] "i2dash" "ComplexHeatmap" "Suggests"
#> [20,] "missoNet" "ComplexHeatmap" "Imports"
#> [21,] "multipanelfigure" "ComplexHeatmap" "Suggests"
#> [22,] "pkgndep" "ComplexHeatmap" "Imports"
#> [23,] "rKOMICS" "ComplexHeatmap" "Imports"
#> [24,] "scITD" "ComplexHeatmap" "Imports"
#> [25,] "spiralize" "ComplexHeatmap" "Suggests"
#> [26,] "tidyHeatmap" "ComplexHeatmap" "Imports"
#> [27,] "tinyarray" "ComplexHeatmap" "Suggests"
#> [28,] "visxhclust" "ComplexHeatmap" "Imports"
#> [29,] "wilson" "ComplexHeatmap" "Imports"
#> [30,] "AMARETTO" "ComplexHeatmap" "Depends"
#> [31,] "ASURAT" "ComplexHeatmap" "Imports"
#> [32,] "BindingSiteFinder" "ComplexHeatmap" "Suggests"
#> [33,] "BioNERO" "ComplexHeatmap" "Imports"
#> [34,] "BiocOncoTK" "ComplexHeatmap" "Imports"
#> [35,] "BloodGen3Module" "ComplexHeatmap" "Imports"
#> [36,] "BrainSABER" "ComplexHeatmap" "Suggests"
#> [37,] "CATALYST" "ComplexHeatmap" "Imports"
#> [38,] "CNVRanger" "ComplexHeatmap" "Suggests"
#> [39,] "COCOA" "ComplexHeatmap" "Imports"
#> [40,] "COTAN" "ComplexHeatmap" "Imports"
#> [41,] "CeTF" "ComplexHeatmap" "Imports"
#> [42,] "DEComplexDisease" "ComplexHeatmap" "Imports"
#> [43,] "DEGreport" "ComplexHeatmap" "Imports"
#> [44,] "DEP" "ComplexHeatmap" "Imports"
#> [45,] "ELMER" "ComplexHeatmap" "Imports"
#> [46,] "EnrichedHeatmap" "ComplexHeatmap" "Depends"
#> [47,] "EnrichmentBrowser" "ComplexHeatmap" "Suggests"
#> [48,] "FLAMES" "ComplexHeatmap" "Imports"
#> [49,] "GRaNIE" "ComplexHeatmap" "Imports"
#> [50,] "GeneTonic" "ComplexHeatmap" "Imports"
#> [51,] "GenomicSuperSignature" "ComplexHeatmap" "Imports"
#> [52,] "HilbertCurve" "ComplexHeatmap" "Suggests"
#> [53,] "InterCellar" "ComplexHeatmap" "Imports"
#> [54,] "InteractiveComplexHeatmap" "ComplexHeatmap" "Depends"
#> [55,] "LineagePulse" "ComplexHeatmap" "Imports"
#> [56,] "MOMA" "ComplexHeatmap" "Imports"
#> [57,] "MWASTools" "ComplexHeatmap" "Imports"
#> [58,] "MatrixQCvis" "ComplexHeatmap" "Imports"
#> [59,] "MesKit" "ComplexHeatmap" "Imports"
#> [60,] "NanoporeRNASeq" "ComplexHeatmap" "Suggests"
#> [61,] "POMA" "ComplexHeatmap" "Imports"
#> [62,] "PathoStat" "ComplexHeatmap" "Imports"
#> [63,] "PeacoQC" "ComplexHeatmap" "Imports"
#> [64,] "QFeatures" "ComplexHeatmap" "Suggests"
#> [65,] "RLSeq" "ComplexHeatmap" "Imports"
#> [66,] "SPIAT" "ComplexHeatmap" "Imports"
#> [67,] "SPONGE" "ComplexHeatmap" "Imports"
#> [68,] "TBSignatureProfiler" "ComplexHeatmap" "Imports"
#> [69,] "TCGAbiolinks" "ComplexHeatmap" "Suggests"
#> [70,] "TCGAutils" "ComplexHeatmap" "Suggests"
#> [71,] "Xeva" "ComplexHeatmap" "Imports"
#> [72,] "YAPSA" "ComplexHeatmap" "Imports"
#> [73,] "airpart" "ComplexHeatmap" "Imports"
#> [74,] "artMS" "ComplexHeatmap" "Suggests"
#> [75,] "bambu" "ComplexHeatmap" "Suggests"
#> [76,] "blacksheepr" "ComplexHeatmap" "Imports"
#> [77,] "celda" "ComplexHeatmap" "Imports"
#> [78,] "clustifyr" "ComplexHeatmap" "Suggests"
#> [79,] "cola" "ComplexHeatmap" "Imports"
#> [80,] "cytoKernel" "ComplexHeatmap" "Imports"
#> [81,] "diffUTR" "ComplexHeatmap" "Imports"
#> [82,] "diffcyt" "ComplexHeatmap" "Imports"
#> [83,] "dittoSeq" "ComplexHeatmap" "Suggests"
#> [84,] "fCCAC" "ComplexHeatmap" "Imports"
#> [85,] "gCrisprTools" "ComplexHeatmap" "Imports"
#> [86,] "gmoviz" "ComplexHeatmap" "Imports"
#> [87,] "gtrellis" "ComplexHeatmap" "Suggests"
#> [88,] "hermes" "ComplexHeatmap" "Imports"
#> [89,] "iSEE" "ComplexHeatmap" "Imports"
#> [90,] "microbiomeMarker" "ComplexHeatmap" "Imports"
#> [91,] "monaLisa" "ComplexHeatmap" "Imports"
#> [92,] "msImpute" "ComplexHeatmap" "Suggests"
#> [93,] "muscat" "ComplexHeatmap" "Imports"
#> [94,] "musicatk" "ComplexHeatmap" "Imports"
#> [95,] "pareg" "ComplexHeatmap" "Suggests"
#> [96,] "pipeComp" "ComplexHeatmap" "Imports"
#> [97,] "plotgardener" "ComplexHeatmap" "Suggests"
#> [98,] "profileplyr" "ComplexHeatmap" "Imports"
#> [99,] "projectR" "ComplexHeatmap" "Suggests"
#> [100,] "proteasy" "ComplexHeatmap" "Suggests"
#> [101,] "recoup" "ComplexHeatmap" "Depends"
#> [102,] "scDblFinder" "ComplexHeatmap" "Suggests"
#> [103,] "sechm" "ComplexHeatmap" "Imports"
#> [104,] "segmenter" "ComplexHeatmap" "Imports"
#> [105,] "signifinder" "ComplexHeatmap" "Imports"
#> [106,] "simplifyEnrichment" "ComplexHeatmap" "Imports"
#> [107,] "singleCellTK" "ComplexHeatmap" "Imports"
#> [108,] "sparrow" "ComplexHeatmap" "Imports"
#> [109,] "spiky" "ComplexHeatmap" "Suggests"
#> [110,] "weitrix" "ComplexHeatmap" "Suggests"
db2$package_dependencies("ComplexHeatmap")
#> package dependency dep_fields
#> [1,] "ComplexHeatmap" "methods" "Depends"
#> [2,] "ComplexHeatmap" "grid" "Depends"
#> [3,] "ComplexHeatmap" "graphics" "Depends"
#> [4,] "ComplexHeatmap" "stats" "Depends"
#> [5,] "ComplexHeatmap" "grDevices" "Depends"
#> [6,] "ComplexHeatmap" "circlize" "Imports"
#> [7,] "ComplexHeatmap" "GetoptLong" "Imports"
#> [8,] "ComplexHeatmap" "colorspace" "Imports"
#> [9,] "ComplexHeatmap" "clue" "Imports"
#> [10,] "ComplexHeatmap" "RColorBrewer" "Imports"
#> [11,] "ComplexHeatmap" "GlobalOptions" "Imports"
#> [12,] "ComplexHeatmap" "png" "Imports"
#> [13,] "ComplexHeatmap" "digest" "Imports"
#> [14,] "ComplexHeatmap" "IRanges" "Imports"
#> [15,] "ComplexHeatmap" "matrixStats" "Imports"
#> [16,] "ComplexHeatmap" "foreach" "Imports"
#> [17,] "ComplexHeatmap" "doParallel" "Imports"
#> [18,] "ComplexHeatmap" "codetools" "Imports"
db2$package_dependencies("ComplexHeatmap", recursive = TRUE)
#> package dependency dep_fields
#> [1,] "ComplexHeatmap" "methods" "Depends"
#> [2,] "ComplexHeatmap" "grid" "Depends"
#> [3,] "ComplexHeatmap" "graphics" "Depends"
#> [4,] "ComplexHeatmap" "stats" "Depends"
#> [5,] "ComplexHeatmap" "grDevices" "Depends"
#> [6,] "ComplexHeatmap" "circlize" "Imports"
#> [7,] "ComplexHeatmap" "GetoptLong" "Imports"
#> [8,] "ComplexHeatmap" "colorspace" "Imports"
#> [9,] "ComplexHeatmap" "clue" "Imports"
#> [10,] "ComplexHeatmap" "RColorBrewer" "Imports"
#> [11,] "ComplexHeatmap" "GlobalOptions" "Imports"
#> [12,] "ComplexHeatmap" "png" "Imports"
#> [13,] "ComplexHeatmap" "digest" "Imports"
#> [14,] "ComplexHeatmap" "IRanges" "Imports"
#> [15,] "ComplexHeatmap" "matrixStats" "Imports"
#> [16,] "ComplexHeatmap" "foreach" "Imports"
#> [17,] "ComplexHeatmap" "doParallel" "Imports"
#> [18,] "ComplexHeatmap" "codetools" "Imports"
#> [19,] "circlize" "graphics" "Depends"
#> [20,] "circlize" "GlobalOptions" "Imports"
#> [21,] "circlize" "shape" "Imports"
#> [22,] "circlize" "grDevices" "Imports"
#> [23,] "circlize" "utils" "Imports"
#> [24,] "circlize" "stats" "Imports"
#> [25,] "circlize" "colorspace" "Imports"
#> [26,] "circlize" "methods" "Imports"
#> [27,] "circlize" "grid" "Imports"
#> [28,] "GetoptLong" "rjson" "Imports"
#> [29,] "GetoptLong" "GlobalOptions" "Imports"
#> [30,] "GetoptLong" "methods" "Imports"
#> [31,] "GetoptLong" "crayon" "Imports"
#> [32,] "colorspace" "methods" "Depends"
#> [33,] "colorspace" "graphics" "Imports"
#> [34,] "colorspace" "grDevices" "Imports"
#> [35,] "colorspace" "stats" "Imports"
#> [36,] "clue" "stats" "Imports"
#> [37,] "clue" "cluster" "Imports"
#> [38,] "clue" "graphics" "Imports"
#> [39,] "clue" "methods" "Imports"
#> [40,] "GlobalOptions" "methods" "Depends"
#> [41,] "GlobalOptions" "utils" "Imports"
#> [42,] "digest" "utils" "Imports"
#> [43,] "IRanges" "methods" "Depends"
#> [44,] "IRanges" "utils" "Depends"
#> [45,] "IRanges" "stats" "Depends"
#> [46,] "IRanges" "BiocGenerics" "Depends"
#> [47,] "IRanges" "S4Vectors" "Depends"
#> [48,] "IRanges" "stats4" "Imports"
#> [49,] "IRanges" "S4Vectors" "LinkingTo"
#> [50,] "foreach" "codetools" "Imports"
#> [51,] "foreach" "utils" "Imports"
#> [52,] "foreach" "iterators" "Imports"
#> [53,] "doParallel" "foreach" "Depends"
#> [54,] "doParallel" "iterators" "Depends"
#> [55,] "doParallel" "parallel" "Depends"
#> [56,] "doParallel" "utils" "Depends"
#> [57,] "shape" "stats" "Imports"
#> [58,] "shape" "graphics" "Imports"
#> [59,] "shape" "grDevices" "Imports"
#> [60,] "crayon" "grDevices" "Imports"
#> [61,] "crayon" "methods" "Imports"
#> [62,] "crayon" "utils" "Imports"
#> [63,] "cluster" "graphics" "Imports"
#> [64,] "cluster" "grDevices" "Imports"
#> [65,] "cluster" "stats" "Imports"
#> [66,] "cluster" "utils" "Imports"
#> [67,] "BiocGenerics" "methods" "Depends"
#> [68,] "BiocGenerics" "utils" "Depends"
#> [69,] "BiocGenerics" "graphics" "Depends"
#> [70,] "BiocGenerics" "stats" "Depends"
#> [71,] "BiocGenerics" "methods" "Imports"
#> [72,] "BiocGenerics" "utils" "Imports"
#> [73,] "BiocGenerics" "graphics" "Imports"
#> [74,] "BiocGenerics" "stats" "Imports"
#> [75,] "S4Vectors" "methods" "Depends"
#> [76,] "S4Vectors" "utils" "Depends"
#> [77,] "S4Vectors" "stats" "Depends"
#> [78,] "S4Vectors" "stats4" "Depends"
#> [79,] "S4Vectors" "BiocGenerics" "Depends"
#> [80,] "iterators" "utils" "Depends"
# }