Package: basejump
Title: Base Functions for Bioinformatics
Description: Toolkit for bioinformatics and R package development.
Version: 0.11.5
Date: 2019-08-11
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 (>= 3.5)
Imports: bioverbs (>= 0.2.4), brio (>= 0.3.2), freerange (>= 0.2.1),
        goalie (>= 0.3.3), syntactic (>= 0.2.3), transformer (>=
        0.2.2), Biobase, BiocGenerics, DelayedArray,
        DelayedMatrixStats, GenomeInfoDb, GenomicRanges, IRanges,
        S4Vectors, SingleCellExperiment, SummarizedExperiment, Matrix
        (>= 1.2), Matrix.utils (>= 0.9), dplyr (>= 0.8), knitr (>=
        1.22), magrittr (>= 1.5), matrixStats (>= 0.54), purrr (>=
        0.3), readr (>= 1.3), reshape2 (>= 1.4), rlang (>= 0.4), scales
        (>= 1.0), sessioninfo (>= 1.1), stringr (>= 1.4), tibble (>=
        2.1), tidyr (>= 0.8), tidyselect (>= 0.2), methods, utils
Suggests: acidroxygen (>= 0.1), acidtest (>= 0.2.2), BiocStyle, DESeq2,
        EnsDb.Hsapiens.v75, biomaRt, patrick (>= 0.0.1), rmarkdown (>=
        1.14), testthat (>= 2.1), viridis (>= 0.5), datasets
Enhances: pbapply (>= 1.4)
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: 'AllClasses.R' 'AllGenerics.R' 'AllGenerators.R'
        'aggregate-methods.R' 'aggregateCellsToSamples-methods.R'
        'alphaThreshold-methods.R' 'autopadZeros-methods.R'
        'calculateMetrics-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' 'globals.R' 'detectLanes.R'
        'estimateSizeFactors-methods.R' 'filterCells-methods.R'
        'geneNames-methods.R' 'geneSynonyms.R'
        'geometricMean-methods.R' 'headtail-methods.R'
        'humanize-methods.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' 'meltCounts-methods.R'
        'metrics-methods.R' 'microplate.R' 'minimalSampleData.R'
        'multiassignAsEnvir.R' 'organism-methods.R' 'package.R'
        'prepareTemplate.R' 'pseudobulk-methods.R' 'rankedMatrix.R'
        'reexports-bioverbs.R' 'reexports-brio.R'
        'reexports-freerange.R' 'reexports-goalie.R'
        'reexports-syntactic.R' 'reexports-transformer.R' 'reexports.R'
        'sampleData-methods.R' 'sampleNames-methods.R'
        'sanitizeSampleData.R' 'selectSamples-methods.R' 'separator.R'
        'show-methods.R' 'showHeader.R' 'showSlotInfo.R'
        'sizeFactors-methods.R' 'sortUnique.R'
        'stripTranscriptVersions-methods.R' 'subsetPerSample-methods.R'
        'summary-methods.R' 'toStringUnique.R'
        'topCellsPerSample-methods.R' 'tpm-methods.R'
        'uniteInterestingGroups-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; ; 2019-08-12 13:30:32 UTC; unix
