Package: basejump
Title: Base Functions for Bioinformatics
Description: Toolkit for bioinformatics and R package development.
Version: 0.11.18
Date: 2019-10-12
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: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.6)
Imports: bioverbs (>= 0.2.10), brio (>= 0.3.10), freerange (>= 0.2.6),
        goalie (>= 0.3.10), syntactic (>= 0.3.1), transformer (>=
        0.2.7), AnnotationDbi (>= 1.46), Biobase (>= 2.44),
        BiocGenerics (>= 0.30), BiocParallel (>= 1.18), Biostrings (>=
        2.52), GenomeInfoDb (>= 1.20), GenomicRanges (>= 1.36), IRanges
        (>= 2.18.2), S4Vectors (>= 0.22), SingleCellExperiment (>=
        1.6), SummarizedExperiment (>= 1.14), biomaRt (>= 2.40), Matrix
        (>= 1.2), Matrix.utils (>= 0.9), knitr (>= 1.24), magrittr (>=
        1.5), matrixStats (>= 0.55), scales (>= 1.0), sessioninfo (>=
        1.1), stringr (>= 1.4), tibble (>= 2.1), methods, utils
Suggests: acidroxygen (>= 0.1.3), acidtest (>= 0.2.5), BiocStyle (>=
        2.12), EnsDb.Hsapiens.v75 (>= 2.99), patrick (>= 0.0.1),
        rmarkdown (>= 1.15), testthat (>= 2.2), datasets
Remotes: acidgenomics/acidplots, acidgenomics/acidroxygen,
        acidgenomics/acidtest, acidgenomics/bioverbs,
        acidgenomics/brio, acidgenomics/freerange, acidgenomics/goalie,
        acidgenomics/syntactic, acidgenomics/transformer
biocViews: DataImport, GenomeAnnotation, Preprocessing
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Collate: 'AllGlobals.R' 'AllClasses.R' 'AllGenerics.R'
        'AllGenerators.R' 'aggregate-methods.R'
        'aggregateCellsToSamples-methods.R' 'alphaThreshold-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' 'counts-methods.R'
        'deprecated.R' 'detectHPC.R' 'detectLanes.R'
        'dottedCase-methods.R' 'estimateSizeFactors-methods.R'
        'filterCells-methods.R' 'geneNames-methods.R' 'geneSynonyms.R'
        'geometricMean-methods.R' 'headtail-methods.R'
        'humanize-methods.R' 'importSampleData.R' 'importTx2Gene.R'
        'imports.R' 'interestingGroups-methods.R' 'internal.R'
        'lfcThreshold-methods.R' 'logRatio-methods.R'
        'makeGene2Symbol.R' 'makeSampleData-methods.R'
        'makeSummarizedExperiment-methods.R'
        'makeSingleCellExperiment-methods.R' 'makeTx2Gene.R'
        'mapCellsToSamples.R' 'mapGenes-methods.R' 'markdown-methods.R'
        'markdownHeader.R' 'markdownLink.R' 'markdownList.R'
        'markdownPlots.R' 'markdownTables.R'
        'matchEnsemblReleaseToURL.R' 'matchHumanOrthologs.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' 'organism-methods.R' 'package.R'
        'prepareTemplate.R' 'pseudobulk-methods.R' 'rankedMatrix.R'
        'reexports-coerce.R' 'reexports.R' 'sampleData-methods.R'
        'sampleNames-methods.R' 'sanitizeSampleData.R'
        'selectSamples-methods.R' 'separator.R' 'showHeader.R'
        'showSlotInfo.R' 'sizeFactors-methods.R' 'snakeCase-methods.R'
        'sortUnique.R' 'stripTranscriptVersions-methods.R'
        'subsetPerSample-methods.R' 'summary-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 3.6.1; ; 2019-10-13 14:15:51 UTC; unix
