Package: basejump
Title: Base Functions for Bioinformatics
Description: Toolkit for bioinformatics and R package development.
Version: 0.9.9
Date: 2019-02-11
Authors@R: c(
    person(
        "Michael", "Steinbaugh",
        email = "mike@steinbaugh.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-2403-2221")
    ),
    person(
        "Rory", "Kirchner",
        email = "roryk@alum.mit.edu",
        role = "ctb",
        comment = c(ORCID = "0000-0003-4814-5885")
    ),
    person(
        given = "Mary",
        family = "Piper",
        email = "mary.piper@gmail.com",
        role = "ctb",
        comment = c(ORCID = "0000-0003-2699-3840")
    ))
URL: https://steinbaugh.com/basejump/,
        https://github.com/steinbaugh/basejump/
BugReports: https://github.com/steinbaugh/basejump/issues/
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: R (>= 3.4)
Imports: bioverbs (>= 0.1.6), brio (>= 0.1.5), goalie (>= 0.2.8),
        syntactic (>= 0.1.4), transformer (>= 0.1.4), AnnotationHub,
        Biobase, BiocGenerics, GenomeInfoDb, GenomicFeatures,
        GenomicRanges, IRanges, Matrix, Matrix.utils, RColorBrewer,
        S4Vectors, SingleCellExperiment, SummarizedExperiment,
        ensembldb, cowplot (>= 0.9), dplyr (>= 0.7), ggplot2 (>= 3.0),
        ggrepel (>= 0.8), knitr (>= 1.21), magrittr (>= 1.5),
        matrixStats (>= 0.54), pheatmap (>= 1.0), purrr (>= 0.2),
        reshape2 (>= 1.4), readr (>= 1.3), rlang (>= 0.3), sessioninfo
        (>= 1.1), stringr (>= 1.3), tibble (>= 2.0), tidyr (>= 0.8),
        tidyselect (>= 0.2), grDevices, grid, methods, stats, utils
Suggests: BiocStyle, EnsDb.Hsapiens.v75, datasets, patrick, rmarkdown,
        testthat, viridis
Enhances: pbapply (>= 1.3)
Remotes: steinbaugh/bioverbs, steinbaugh/brio, steinbaugh/goalie,
        steinbaugh/syntactic, steinbaugh/transformer
biocViews: DataImport, GenomeAnnotation, Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Collate: 'AllClasses.R' 'AllGenerics.R' 'EggNOG.R'
        'Ensembl2Entrez-methods.R' 'Gene2Symbol-methods.R'
        'HGNC2Ensembl.R' 'MGI2Ensembl.R' 'PANTHER.R'
        'Tx2Gene-methods.R' 'aggregate-methods.R'
        'aggregateCellsToSamples-methods.R' 'autopadZeros-methods.R'
        'cell2sample-methods.R' 'collapseToString-methods.R'
        'combine-methods.R' 'convertGenesToSymbols-methods.R'
        'convertSampleIDsToNames-methods.R'
        'convertTranscriptsToGenes-methods.R'
        'convertUCSCBuildToEnsembl.R' 'counts-methods.R' 'data.R'
        'deprecated.R' 'detectHPC.R' 'detectLanes.R' 'detectOrganism.R'
        'emptyRanges.R' 'geneNames-methods.R' 'geneSynonyms.R'
        'geometricMean-methods.R' 'ggplot2.R' 'globals.R'
        'headtail-methods.R' 'humanize-methods.R' 'imports.R'
        'interestingGroups-methods.R' 'internal.R' 'logRatio-methods.R'
        'makeGRanges-methods.R' 'makeGene2Symbol-methods.R'
        'makeSampleData.R' 'makeSingleCellExperiment.R'
        'makeSummarizedExperiment.R' 'makeTx2Gene-methods.R'
        'mapCellsToSamples.R' 'mapGenes-methods.R' 'markdown-methods.R'
        'markdownHeader.R' 'markdownLink.R' 'markdownList.R'
        'markdownPlots.R' 'markdownTables.R' 'matchInterestingGroups.R'
        'matchesGene2Symbol.R' 'matchesInterestingGroups.R'
        'meltCounts-methods.R' 'metrics-methods.R' 'microplate.R'
        'minimalSampleData.R' 'multiassignAsEnvir.R'
        'organism-methods.R' 'package.R' 'params.R'
        'plotCounts-methods.R' 'plotCountsPerBiotype-methods.R'
        'plotCountsPerGene-methods.R' 'plotGenderMarkers-methods.R'
        'plotGenesDetected-methods.R' 'plotHeatmap-methods.R'
        'plotPCA-methods.R' 'plotQC-methods.R'
        'plotTotalCounts-methods.R' 'plotZerosVsDepth-methods.R'
        'prepareTemplate.R' 'reexports-brio.R' 'reexports-goalie.R'
        'reexports-syntactic.R' 'reexports-transformer.R' 'reexports.R'
        'relevel.R' 'removeNA-methods.R' 'sampleData-methods.R'
        'sampleNames-methods.R' 'sanitizeNA-methods.R'
        'sanitizePercent-methods.R' 'sanitizeSampleData.R'
        'selectSamples-methods.R' 'separator.R' 'show-methods.R'
        'showSlotInfo.R' 'stripTranscriptVersions-methods.R'
        'subsetPerSample-methods.R' 'summary-methods.R'
        'topCellsPerSample-methods.R' 'tpm-methods.R' 'unique.R'
        'uniteInterestingGroups-methods.R' 'zerosVsDepth-methods.R'
Author: Michael Steinbaugh [aut, cre] (<https://orcid.org/0000-0002-2403-2221>),
  Rory Kirchner [ctb] (<https://orcid.org/0000-0003-4814-5885>),
  Mary Piper [ctb] (<https://orcid.org/0000-0003-2699-3840>)
Maintainer: Michael Steinbaugh <mike@steinbaugh.com>
Built: R 3.5.1; ; 2019-02-14 12:57:24 UTC; unix
