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manifest.json
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"Title": "Efficient manipulation of biological strings",
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"git_url": "https://git.bioconductor.org/packages/Biostrings",
"git_branch": "RELEASE_3_15",
"git_last_commit": "c7ad3c7",
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"NeedsCompilation": "yes",
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"description": {
"Package": "DBI",
"Title": "R Database Interface",
"Version": "1.1.2",
"Date": "2021-12-19",
"Authors@R": "c(\n person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"),\n person(\"Hadley\", \"Wickham\", role = \"aut\"),\n person(\"Kirill\", \"Müller\", , \"[email protected]\", role = c(\"aut\", \"cre\"),\n comment = c(ORCID = \"0000-0002-1416-3412\")),\n person(\"R Consortium\", role = \"fnd\")\n )",
"Description": "A database interface definition for communication between R\n and relational database management systems. All classes in this\n package are virtual and need to be extended by the various R/DBMS\n implementations.",
"License": "LGPL (>= 2.1)",
"URL": "https://dbi.r-dbi.org, https://github.com/r-dbi/DBI",
"BugReports": "https://github.com/r-dbi/DBI/issues",
"Depends": "methods, R (>= 3.0.0)",
"Suggests": "blob, covr, DBItest, dbplyr, downlit, dplyr, glue, hms,\nknitr, magrittr, RMariaDB, rmarkdown, rprojroot, RSQLite (>=\n1.1-2), testthat, xml2",
"VignetteBuilder": "knitr",
"Config/autostyle/scope": "line_breaks",
"Config/autostyle/strict": "false",
"Config/Needs/check": "r-dbi/DBItest",
"Encoding": "UTF-8",
"RoxygenNote": "7.1.2",
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"NeedsCompilation": "no",
"Packaged": "2021-12-19 20:43:28 UTC; kirill",
"Author": "R Special Interest Group on Databases (R-SIG-DB) [aut],\n Hadley Wickham [aut],\n Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),\n R Consortium [fnd]",
"Maintainer": "Kirill Müller <[email protected]>",
"Repository": "CRAN",
"Date/Publication": "2021-12-20 08:32:06 UTC",
"Built": "R 4.2.0; ; 2022-04-25 03:38:59 UTC; unix"
}
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"Source": "Bioconductor",
"Repository": "https://bioconductor.org/packages/3.15/bioc/src/contrib",
"GithubRepo": null,
"GithubUsername": null,
"GithubRef": null,
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"description": {
"Package": "DECIPHER",
"Type": "Package",
"Title": "Tools for curating, analyzing, and manipulating biological\nsequences",
"Version": "2.24.0",
"Date": "2022-04-25",
"Author": "Erik Wright",
"Maintainer": "Erik Wright <[email protected]>",
"biocViews": "Clustering, Genetics, Sequencing, DataImport, Visualization,\nMicroarray, QualityControl, qPCR, Alignment, WholeGenome,\nMicrobiome, ImmunoOncology, GenePrediction",
"Description": "A toolset for deciphering and managing biological sequences.",
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"Imports": "methods, DBI, S4Vectors, IRanges, XVector",
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"License": "GPL-3",
"ByteCompile": "true",
"git_url": "https://git.bioconductor.org/packages/DECIPHER",
"git_branch": "RELEASE_3_15",
"git_last_commit": "437e600",
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"Date/Publication": "2022-04-26",
"NeedsCompilation": "yes",
"Packaged": "2022-04-26 22:11:30 UTC; biocbuild",
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}
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"description": {
"Package": "DT",
"Type": "Package",
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"Description": "'Rcpp' integration for 'GNU GSL' vectors and matrices\n The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for\n scientific computing. It is particularly useful for C and C++ programs as it\n provides a standard C interface to a wide range of mathematical routines. There\n are over 1000 functions in total with an extensive test suite. The 'RcppGSL'\n package provides an easy-to-use interface between 'GSL' data structures and\n R using concepts from 'Rcpp' which is itself a package that eases the\n interfaces between R and C++. This package also serves as a prime example of\n how to build a package that uses 'Rcpp' to connect to another third-party\n library. The 'autoconf' script, 'inline' plugin and example package can all\n be used as a stanza to write a similar package against another library.",
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"Type": "Package",
"Title": "'Rcpp' Integration of Different \"Ziggurat\" Normal RNG\nImplementations",
"Version": "0.1.6",
"Date": "2020-10-18",
"Author": "Dirk Eddelbuettel",
"Maintainer": "Dirk Eddelbuettel <[email protected]>",
"Description": "The Ziggurat generator for normally distributed random\n numbers, originally proposed by Marsaglia and Tsang (2000, \n <doi:10.18637/jss.v005.i08>) has been improved upon a few times\n starting with Leong et al (2005, <doi:10.18637/jss.v012.i07>).\n This package provides an aggregation in order to compare different\n implementations in order to provide an 'faster but good enough'\n alternative for use with R and C++ code.",
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"Packaged": "2020-10-18 11:56:11 UTC; edd",
"Repository": "CRAN",
"Date/Publication": "2020-10-20 07:30:02 UTC",
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"Title": "Update and Manipulate Rd Documentation Objects",
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"Date": "2022-03-22",
"Authors@R": "c( person(given = c(\"Georgi\", \"N.\"),\n family = \"Boshnakov\", \n role = c(\"aut\", \"cre\"), \n email = \"[email protected]\"), \n\t person(given = \"Duncan\", \n\t family = \"Murdoch\", \n\t role = \"ctb\", email = \"[email protected]\") )",
"Description": "Functions for manipulation of R documentation objects,\n including functions reprompt() and ereprompt() for updating 'Rd'\n documentation for functions, methods and classes; 'Rd' macros for\n citations and import of references from 'bibtex' files for use in\n 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and\n inserting snippets of 'R' code and the results of its evaluation or\n creating graphics on the fly; and many functions for manipulation of\n references and Rd files.",
"URL": "https://geobosh.github.io/Rdpack/ (website),\nhttps://github.com/GeoBosh/Rdpack (devel)",
"BugReports": "https://github.com/GeoBosh/Rdpack/issues",
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"Author": "Georgi N. Boshnakov [aut, cre],\n Duncan Murdoch [ctb]",
"Maintainer": "Georgi N. Boshnakov <[email protected]>",
"Repository": "CRAN",
"Date/Publication": "2022-03-23 07:50:30 UTC",
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"Package": "Rfast",
"Type": "Package",
"Title": "A Collection of Efficient and Extremely Fast R Functions",
"Version": "2.0.6",
"Date": "2022-02-15",
"Author": "Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.",
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"SystemRequirements": "C++17",
"BugReports": "https://github.com/RfastOfficial/Rfast/issues",
"URL": "https://github.com/RfastOfficial/Rfast",
"Description": "A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. ",
"License": "GPL (>= 2.0)",
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"Packaged": "2022-02-15 12:42:26 UTC; epapadakis",
"Repository": "CRAN",
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"Title": "Identify Rogue Taxa in Sets of Phylogenetic Trees",
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"License": "GPL (>= 3)",
"Description": "Rogue (\"wildcard\") taxa are leaves with uncertain phylogenetic\n position.\n Their position may vary from tree to tree under inference methods that yield a\n tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).\n The presence of rogue taxa in a tree set can potentially remove all\n information from a consensus tree. The information content of a consensus\n tree - a function of its resolution and branch support values - can often be\n increased by removing rogue taxa. \n 'Rogue' provides an explicitly information-theoretic approach to rogue\n detection (Smith 2022) <doi:10.1093/sysbio/syab099>,\n and an interface to 'RogueNaRok' (Aberer et al. 2013)\n <doi:10.1093/sysbio/sys078>.",
"URL": "https://github.com/ms609/Rogue/,\nhttps://github.com/aberer/RogueNaRok/,\nhttps://github.com/ms609/RogueNaRok/",
"BugReports": "https://github.com/ms609/Rogue/issues/",
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"Imports": "ape (>= 5.0), cli (>= 3.0), fastmatch, grDevices, matrixStats,\nRdpack (>= 0.7), Rfast, stats, TreeDist (> 2.2.0), TreeTools\n(>= 1.6.0), utils,",
"Suggests": "knitr, rmarkdown, spelling, testthat,",
"Config/Needs/github-actions": "callr, pkgbuild, rcmdcheck,",
"Config/Needs/coverage": "covr",
"Config/Needs/memcheck": "devtools",
"Config/Needs/metadata": "codemetar",
"Config/Needs/website": "pkgdown",
"RdMacros": "Rdpack",
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"ByteCompile": "true",
"Encoding": "UTF-8",
"Language": "en-GB",
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"Packaged": "2022-01-13 10:00:11 UTC; pjjg18",
"Author": "Martin R. Smith [aut, cre, cph]\n (<https://orcid.org/0000-0001-5660-1727>),\n Andre J. Aberer [aut, cph]",
"Maintainer": "Martin R. Smith <[email protected]>",
"Repository": "CRAN",
"Date/Publication": "2022-01-13 12:02:46 UTC",
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"description": {
"Package": "Rttf2pt1",
"Title": "'ttf2pt1' Program",
"Version": "1.3.10",
"Author": "Winston Chang,\n Andrew Weeks,\n Frank M. Siegert,\n Mark Heath,\n Thomas Henlick,\n Sergey Babkin,\n Turgut Uyar,\n Rihardas Hepas,\n Szalay Tamas,\n Johan Vromans,\n Petr Titera,\n Lei Wang,\n Chen Xiangyang,\n Zvezdan Petkovic,\n Rigel,\n I. Lee Hetherington",
"Maintainer": "Winston Chang <[email protected]>",
"Description": "Contains the program 'ttf2pt1', for use with the\n 'extrafont' package. This product includes software developed by the 'TTF2PT1'\n Project and its contributors.",
"Depends": "R (>= 2.15)",
"License": "file LICENSE",