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DUD data can be downloaded using the \"DUD()\" function in ChemmineR.", "biocViews": [ "AnnotationData", "CustomDBSchema" ], "Author": "Kevin Horan", "Maintainer": "Kevin Horan ", "VignetteBuilder": "knitr", "source.ver": "src/contrib/ChemmineDrugs_1.0.2.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "suggestsMe": [ "ChemmineR" ], "dependencyCount": "82", "Rank": 197 }, "chicken.db": { "Package": "chicken.db", "Version": "3.13.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.53.2)", "org.Gg.eg.db (>= 3.13.0)" ], "Imports": [ "methods", "AnnotationDbi" ], "Suggests": [ "DBI", "annotate", "RUnit" ], "License": "Artistic-2.0", "MD5sum": "512f887df339529d4883aad3f3eb6fb8", "NeedsCompilation": "no", "Title": "Affymetrix Affymetrix Chicken Array annotation data (chip chicken)", "Description": "Affymetrix Affymetrix Chicken Array annotation data (chip chicken) assembled using data from public repositories", "biocViews": [ "AffymetrixChip", "AnnotationData", "ChipDb", "Gallus_gallus", "chicken" ], "Author": "Marc Carlson", "Maintainer": "Bioconductor Package Maintainer ", "organism": "Gallus gallus", "manufacturer": "Affymetrix", "source.ver": "src/contrib/chicken.db_3.13.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "47", "Rank": 483 }, "chicken.db0": { "Package": "chicken.db0", "Version": "3.18.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.63.2)" ], "License": "Artistic-2.0", "MD5sum": "0f0c20a519a9490c0909b68ec67c206d", "NeedsCompilation": "no", "Title": "Base Level Annotation databases for chicken", "Description": "Base annotation databases for chicken, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.", "biocViews": [ "AnnotationData", "Gallus_gallus", "db0" ], "Author": "Bioconductor Core Team", "Maintainer": "Bioconductor Package Maintainer ", "organism": "Gallus gallus", "source.ver": "src/contrib/chicken.db0_3.18.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "46", "Rank": 627 }, "chickencdf": { "Package": "chickencdf", "Version": "2.18.0", "Depends": [ "utils" ], "Imports": [ "AnnotationDbi" ], "License": "LGPL", "MD5sum": "ab0097b4b7b6c4d94360feb84ab69972", "NeedsCompilation": "no", "Title": "chickencdf", "Description": "A package containing an environment representing the Chicken.cdf file.", "biocViews": [ "AffymetrixChip", "AnnotationData", "Gallus_gallus", "cdf", "chicken" ], "Author": "The Bioconductor Project", "Maintainer": "Bioconductor Package Maintainer ", "source.ver": "src/contrib/chickencdf_2.18.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "46", "Rank": 627 }, "chickenprobe": { "Package": "chickenprobe", "Version": "2.18.0", "Depends": [ "R (>= 1.6)", "AnnotationDbi (>= 1.11.21)" ], "License": "LGPL", "MD5sum": "b33599081ce1ba768ff7992e143c01d0", "NeedsCompilation": "no", "Title": "Probe sequence data for microarrays of type chicken", "Description": "This package was automatically created by package AnnotationForge version 1.11.21. 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The probe sequence data was obtained from http://www.affymetrix.com. The file name was Citrus\\_probe\\_tab.", "biocViews": [ "AffymetrixChip", "AnnotationData", "Citrus_sp", "citrus", "probe" ], "Author": "The Bioconductor Project www.bioconductor.org", "Maintainer": "Bioconductor Package Maintainer ", "source.ver": "src/contrib/citrusprobe_2.18.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "46", "Rank": 627 }, "clariomdhumanprobeset.db": { "Package": "clariomdhumanprobeset.db", "Version": "8.8.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.53.2)", "org.Hs.eg.db (>= 3.13.0)" ], "Imports": [ "methods", "AnnotationDbi" ], "Suggests": [ "DBI", "annotate", "RUnit" ], "License": "Artistic-2.0", "MD5sum": "01cb1a5cc4674750b6ce5988cd62fad3", "NeedsCompilation": "no", "Title": "Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset)", "Description": "Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) assembled using data from public repositories", "biocViews": [ "AffymetrixChip", "AnnotationData", "ChipDb", "Homo_sapiens", "clariomdhumanprobeset" ], "Author": "James W. 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MacDonald", "Maintainer": "Biocore Package Maintainer ", "organism": "Homo sapiens", "manufacturer": "Affymetrix", "source.ver": "src/contrib/clariomshumanhttranscriptcluster.db_8.8.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "47", "Rank": 438 }, "clariomshumantranscriptcluster.db": { "Package": "clariomshumantranscriptcluster.db", "Version": "8.8.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.53.2)", "org.Hs.eg.db (>= 3.13.0)" ], "Imports": [ "methods", "AnnotationDbi" ], "Suggests": [ "DBI", "annotate", "RUnit" ], "License": "Artistic-2.0", "MD5sum": "309b29e044e1227da6d4825bbdf04b76", "NeedsCompilation": "no", "Title": "Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster)", "Description": "Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) assembled using data from public repositories", "biocViews": [ "AffymetrixChip", "AnnotationData", "ChipDb", "Homo_sapiens", "clariomshumantranscriptcluster" ], "Author": "James W. MacDonald", "Maintainer": "Biocore Package Maintainer ", "organism": "Homo sapiens", "manufacturer": "Affymetrix", "source.ver": "src/contrib/clariomshumantranscriptcluster.db_8.8.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "47", "Rank": 269 }, "clariomsmousehttranscriptcluster.db": { "Package": "clariomsmousehttranscriptcluster.db", "Version": "8.8.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.53.2)", "org.Mm.eg.db (>= 3.13.0)" ], "Imports": [ "methods", "AnnotationDbi" ], "Suggests": [ "DBI", "annotate", "RUnit" ], "License": "Artistic-2.0", "MD5sum": "c0aa96cbd5ee7e19296dde5a72232d17", "NeedsCompilation": "no", "Title": "Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster)", "Description": "Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories", "biocViews": [ "AffymetrixChip", "AnnotationData", "ChipDb", "Mus_musculus", "clariomsmousehttranscriptcluster" ], "Author": "James W. 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MacDonald", "Maintainer": "Biocore Package Maintainer ", "organism": "Mus musculus", "manufacturer": "Affymetrix", "source.ver": "src/contrib/clariomsmousetranscriptcluster.db_8.8.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "47", "Rank": 253 }, "clariomsrathttranscriptcluster.db": { "Package": "clariomsrathttranscriptcluster.db", "Version": "8.8.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.53.2)", "org.Rn.eg.db (>= 3.13.0)" ], "Imports": [ "methods", "AnnotationDbi" ], "Suggests": [ "DBI", "annotate", "RUnit" ], "License": "Artistic-2.0", "MD5sum": "e7c71721f8201bfd1553a98cfbf47458", "NeedsCompilation": "no", "Title": "Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster)", "Description": "Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) assembled using data from public repositories", "biocViews": [ "AffymetrixChip", "AnnotationData", "ChipDb", "Rattus_norvegicus", "clariomsrathttranscriptcluster" ], "Author": "James W. MacDonald", "Maintainer": "Biocore Package Maintainer ", "organism": "Rattus norvegicus", "manufacturer": "Affymetrix", "source.ver": "src/contrib/clariomsrathttranscriptcluster.db_8.8.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "47", "Rank": 549 }, "clariomsrattranscriptcluster.db": { "Package": "clariomsrattranscriptcluster.db", "Version": "8.8.0", "Depends": [ "R (>= 2.7.0)", "methods", "AnnotationDbi (>= 1.53.2)", "org.Rn.eg.db (>= 3.13.0)" ], "Imports": [ "methods", "AnnotationDbi" ], "Suggests": [ "DBI", "annotate", "RUnit" ], "License": "Artistic-2.0", "MD5sum": "72923a3a90f2df27a361b1730cfc0d00", "NeedsCompilation": "no", "Title": "Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster)", "Description": "Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) assembled using data from public repositories", "biocViews": [ "AffymetrixChip", "AnnotationData", "ChipDb", "Rattus_norvegicus", "clariomsrattranscriptcluster" ], "Author": "James W. MacDonald", "Maintainer": "Biocore Package Maintainer ", "organism": "Rattus norvegicus", "manufacturer": "Affymetrix", "source.ver": "src/contrib/clariomsrattranscriptcluster.db_8.8.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "47", "Rank": 549 }, "cMAP": { "Package": "cMAP", "Version": "1.15.1", "Depends": [ "R(>= 2.4.0)" ], "License": "LGPL", "MD5sum": "dbf8df4d4540151936884e1c5d747bcf", "NeedsCompilation": "no", "Title": "A data package containing annotation data for cMAP", "Description": "Annotation data file for cMAP assembled using data from public data repositories", "Author": "Ting-Yuan Liu, ChenWei Lin, Seth Falcon, Jianhua Zhang, James W. MacDonald", "Maintainer": "Biocore Data Team ", "source.ver": "src/contrib/cMAP_1.15.1.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependsOnMe": [ "pathRender" ], "dependencyCount": "0", "Rank": 168, "biocViews": [ "AnnotationData" ] }, "cottoncdf": { "Package": "cottoncdf", "Version": "2.18.0", "Depends": [ "utils" ], "Imports": [ "AnnotationDbi" ], "License": "LGPL", "MD5sum": "b9d2a4b43235c6e531b78cca006e84b2", "NeedsCompilation": "no", "Title": "cottoncdf", "Description": "A package containing an environment representing the Cotton.cdf file.", "biocViews": [ "AffymetrixChip", "AnnotationData", "Gossypium_arboretum", "Gossypium_barbadense", "Gossypium_hirsutum", "Gossypium_raimondii", "cdf", "cotton" ], "Author": "The Bioconductor Project", "Maintainer": "Bioconductor Package Maintainer ", "source.ver": "src/contrib/cottoncdf_2.18.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "46", "Rank": 724 }, "cottonprobe": { "Package": "cottonprobe", "Version": "2.18.0", "Depends": [ "R (>= 1.6)", "AnnotationDbi (>= 1.11.21)" ], "License": "LGPL", "MD5sum": "032fa94876685820d94526fd56dd0b65", "NeedsCompilation": "no", "Title": "Probe sequence data for microarrays of type cotton", "Description": "This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Cotton\\_probe\\_tab.", "biocViews": [ "AffymetrixChip", "AnnotationData", "Gossypium_arboretum", "Gossypium_barbadense", "Gossypium_hirsutum", "Gossypium_raimondii", "cotton", "probe" ], "Author": "The Bioconductor Project www.bioconductor.org", "Maintainer": "Bioconductor Package Maintainer ", "source.ver": "src/contrib/cottonprobe_2.18.0.tar.gz", "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "dependencyCount": "46", "Rank": 724 }, "CTCF": { "Package": "CTCF", "Version": "0.99.11", "Suggests": [ "BiocStyle", "rmarkdown", "knitr", "AnnotationHub", "GenomicRanges", "plyranges", "sessioninfo" ], "License": "MIT + file LICENSE", "MD5sum": "5ec44245864395de390e68fa56e465af", "NeedsCompilation": "no", "Title": "Genomic coordinates of CTCF binding sites, with orientation", "Description": "Genomic coordinates of CTCF binding sites, with strand orientation (directionality of binding). Position weight matrices (PWMs) from JASPAR, HOCOMOCO, CIS-BP, CTCFBSDB, SwissRegulon, Jolma 2013, were used to uniformly predict CTCF binding sites using FIMO (default settings) on human (hg18, hg19, hg38, T2T) and mouse (mm9, mm10, mm39) genome assemblies. Extra columns include motif/PWM name (e.g., MA0139.1), score, p-value, q-value, and the motif sequence. It is recommended to filter FIMO-predicted sites by 1e-6 p-value threshold instead of using the default 1e-4 threshold. Experimentally obtained CTCF-bound cis-regulatory elements from ENCODE SCREEN and predicted CTCF sites from CTCFBSDB are also included. Selected data are lifted over from a different genome assembly as we demonstrated liftOver is a viable option to obtain CTCF coordinates in different genome assemblies. 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To search this databases, please use the package TFBSTools (>= 1.15.6).", "biocViews": [ "AnnotationData", "FunctionalAnnotation" ], "Author": "Ge Tan ", "Maintainer": "Ge Tan ", "URL": "http://jaspar.genereg.net/", "source.ver": "src/contrib/JASPAR2018_1.1.1.tar.gz", "hasREADME": false, "hasNEWS": true, "hasINSTALL": false, "hasLICENSE": false, "importsMe": [ "enrichTF", "esATAC", "primirTSS" ], "suggestsMe": [ "MAGAR", "pageRank", "TFBSTools" ], "dependencyCount": "1", "Rank": 54 }, "JASPAR2020": { "Package": "JASPAR2020", "Version": "0.99.10", "Depends": [ "R (>= 3.6.0)", "methods" ], "Suggests": [ "knitr", "rmarkdown", "TFBSTools (>= 1.23.1)" ], "License": "GPL-2", "MD5sum": "bfcaf41ebf0935b8d146afd37719de2d", "NeedsCompilation": "no", "Title": "Data package for JASPAR database (version 2020)", "Description": "Data package for JASPAR2020. To search this databases, please use the package TFBSTools (>= 1.23.1).", "biocViews": [ "AnnotationData", "FunctionalAnnotation" ], "Author": "Damir Baranasic ", "Maintainer": "Damir Baranasic ", "URL": "http://jaspar.genereg.net/", "VignetteBuilder": "knitr", "source.ver": "src/contrib/JASPAR2020_0.99.10.tar.gz", "vignettes": [ "vignettes/JASPAR2020/inst/doc/JASPAR2020.html" ], "vignetteTitles": [ "JASPAR2020" ], "hasREADME": false, "hasNEWS": false, "hasINSTALL": false, "hasLICENSE": false, "Rfiles": [ "vignettes/JASPAR2020/inst/doc/JASPAR2020.R" ], "suggestsMe": [ "monaLisa", "motifStack" ], "dependencyCount": "1", "Rank": 22 }, "JASPAR2022": { "Package": "JASPAR2022", "Version": "0.99.7", "Depends": [ "R (>= 4.1.0)", "methods", "BiocFileCache", "utils" ], "Suggests": [ "knitr", "rmarkdown", "BiocStyle", "TFBSTools (>= 1.31.2)" ], "License": "GPL-2", "MD5sum": "282af23228198a377fa9bd76c94dd5eb", "NeedsCompilation": "no", "Title": "Data package for JASPAR database (version 2022)", "Description": "JASPAR is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. 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In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20 percent increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF-binding sites in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. 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The source data files used for this package were created by NCBI between November 8-12, 2016, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be \"injected\" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.", "biocViews": [ "AnnotationData", "Genetics", "Homo_sapiens", "SNPlocs" ], "Author": "Hervé Pagès", "Maintainer": "H. 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