Package: basejump
Title: Base Functions for Bioinformatics
Description: Toolkit for bioinformatics and R package development.
Version: 0.13.4
Date: 2020-12-04
Authors@R: c(
    person(
        "Michael", "Steinbaugh",
        email = "mike@steinbaugh.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-2403-2221")
    ),
    person(
        given = "Acid Genomics",
        role = c("cph", "fnd")
    ),
    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://basejump.acidgenomics.com/,
        https://github.com/acidgenomics/basejump/
BugReports: https://github.com/acidgenomics/basejump/issues/
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: AcidBase (>= 0.2.4), AcidGenerics (>= 0.4.1), AcidGenomes (>=
        0.1.1), AcidPlyr (>= 0.1.4), Biobase, BiocGenerics, Biostrings,
        GenomicRanges, IRanges, Matrix (>= 1.2), S4Vectors,
        SingleCellExperiment, SummarizedExperiment, cli (>= 2.2),
        goalie (>= 0.4.11), magrittr (>= 2.0), matrixStats (>= 0.57),
        methods, pipette (>= 0.4.19), scales (>= 1.1), sessioninfo (>=
        1.1), stringr (>= 1.4), syntactic (>= 0.4.3), tibble (>= 3.0),
        utils
Suggests: AcidTest (>= 0.4.0), BiocStyle, datasets, knitr, rmarkdown,
        testthat
biocViews: DataImport, GenomeAnnotation, Preprocessing
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Additional_repositories: https://r.acidgenomics.com
Collate: 'AllGlobals.R' 'AllClasses.R' 'AllGenerics.R'
        'aggregate-methods.R' 'aggregateCellsToSamples-methods.R'
        'aggregateCols-methods.R' 'aggregateRows-methods.R'
        'autopadZeros-methods.R' 'calculateMetrics-methods.R'
        'camelCase-methods.R' 'cell2sample-methods.R'
        'collapseToString-methods.R' 'combine-methods.R'
        'convertGenesToSymbols-methods.R'
        'convertSampleIDsToNames-methods.R'
        'convertTranscriptsToGenes-methods.R' 'correlation-methods.R'
        'counts-methods.R' 'deprecated.R' 'detectHPC.R' 'detectLanes.R'
        'dottedCase-methods.R' 'estimateSizeFactors-methods.R'
        'filterCells-methods.R' 'geometricMean-methods.R'
        'headtail-methods.R' 'humanize-methods.R' 'importSampleData.R'
        'imports.R' 'integerCounts-methods.R'
        'interestingGroups-methods.R' 'internal.R'
        'intersectAll-methods.R' 'intersectionMatrix-methods.R'
        'logRatio-methods.R' 'makeSampleData-methods.R'
        'makeSingleCellExperiment.R' 'makeSummarizedExperiment.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'
        'mcolnames-methods.R' 'melt-methods.R' 'metrics-methods.R'
        'microplate.R' 'minimalSampleData.R' 'multiassignAsEnvir.R'
        'nonzeroRowsAndCols-methods.R' 'package.R' 'prepareTemplate.R'
        'rankedMatrix.R' 'reexports-classes.R' 'reexports-coerce.R'
        'reexports.R' 'sampleData-methods.R' 'sampleNames-methods.R'
        'sanitizeSampleData.R' 'selectSamples-methods.R'
        'sem-methods.R' 'separator.R' 'showHeader.R'
        'sizeFactors-methods.R' 'snakeCase-methods.R' 'sortUnique.R'
        'subsetPerSample-methods.R' 'toStringUnique.R'
        'topCellsPerSample-methods.R' 'tpm-methods.R'
        'uniteInterestingGroups-methods.R' 'upperCamelCase-methods.R'
        'zerosVsDepth-methods.R'
Author: Michael Steinbaugh [aut, cre] (<https://orcid.org/0000-0002-2403-2221>),
  Acid Genomics [cph, fnd],
  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 4.0.3; ; 2020-12-08 12:09:14 UTC; unix
