Package: basejump
Title: Base Functions for Bioinformatics
Description: Toolkit for bioinformatics and R package development.
Version: 0.12.5
Date: 2020-03-16
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 (>= 3.6)
Imports: AnnotationDbi (>= 1.48), AnnotationHub (>= 2.18), Biobase (>=
        2.46), BiocGenerics (>= 0.32), BiocParallel (>= 1.20),
        Biostrings (>= 2.54), GenomeInfoDb (>= 1.22), GenomicFeatures
        (>= 1.38), GenomicRanges (>= 1.38), IRanges (>= 2.20), Matrix
        (>= 1.2), RCurl (>= 1.95), R.utils (>= 2.9), S4Vectors (>=
        0.24), SingleCellExperiment (>= 1.8), SummarizedExperiment (>=
        1.16), acidbase (>= 0.1.5), acidgenerics (>= 0.3.4), biomaRt
        (>= 2.42), cli (>= 2.0), ensembldb (>= 2.10), goalie (>=
        0.4.2), knitr (>= 1.26), magrittr (>= 1.5), matrixStats (>=
        0.55), pipette (>= 0.4.1), scales (>= 1.1), sessioninfo (>=
        1.1), stringr (>= 1.4), syntactic (>= 0.3.8), tibble (>= 2.1),
        methods, utils
Suggests: BiocStyle (>= 2.14), EnsDb.Hsapiens.v75 (>= 2.99),
        acidroxygen (>= 0.1.8), acidtest (>= 0.3.0), patrick (>=
        0.0.1), rmarkdown (>= 2.0), testthat (>= 2.3), datasets
Remotes: acidgenomics/acidbase, acidgenomics/acidgenerics,
        acidgenomics/acidroxygen, acidgenomics/acidtest,
        acidgenomics/goalie, acidgenomics/pipette,
        acidgenomics/syntactic, acidgenomics/transformer
biocViews: DataImport, GenomeAnnotation, Preprocessing
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.0
VignetteBuilder: knitr
Collate: 'AllGlobals.R' 'AllClasses.R' 'AllGenerics.R'
        'Ensembl2Entrez-methods.R' 'Gene2Symbol-methods.R'
        'HGNC2Ensembl.R' 'MGI2Ensembl.R' 'Tx2Gene-methods.R'
        'TxDb-internal.R' 'aggregate-methods.R'
        'aggregateCellsToSamples-methods.R' 'aggregateCols-methods.R'
        'aggregateRows-methods.R' 'alphaThreshold-methods.R'
        'autopadZeros-methods.R' 'broadClass-internal.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'
        'convertUCSCBuildToEnsembl.R' 'correlation-methods.R'
        'counts-methods.R' 'currentGenomeVersions.R' 'deprecated.R'
        'detectGFF-internal.R' 'detectHPC.R' 'detectLanes.R'
        'detectOrganism.R' 'dottedCase-methods.R' 'emptyRanges.R'
        'estimateSizeFactors-methods.R' 'filterCells-methods.R'
        'geneNames-methods.R' 'geneSynonyms.R'
        'geometricMean-methods.R' 'getURLDirList.R'
        'headtail-methods.R' 'humanize-methods.R' 'importSampleData.R'
        'importTx2Gene.R' 'imports.R' 'integerCounts-methods.R'
        'interestingGroups-methods.R' 'internal.R' 'join-methods.R'
        'lfcThreshold-methods.R' 'logRatio-methods.R'
        'makeGRanges-internal.R' 'makeGRangesFromEnsembl.R'
        'makeGRangesFromEnsDb.R' 'makeGRangesFromGFF-Ensembl.R'
        'makeGRangesFromGFF-FlyBase.R' 'makeGRangesFromGFF-GENCODE.R'
        'makeGRangesFromGFF-RefSeq.R' 'makeGRangesFromGFF-WormBase.R'
        'makeGRangesFromGFF.R' 'makeGene2Symbol.R'
        'makeSampleData-methods.R' 'makeSummarizedExperiment-methods.R'
        'makeSingleCellExperiment-methods.R' 'makeTx2Gene.R'
        'makeTx2GeneFromFASTA.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'
        'mergeGenesIntoTranscripts-internal.R' 'metrics-methods.R'
        'microplate.R' 'minimalSampleData.R' 'multiassignAsEnvir.R'
        'mutate-methods.R' 'nonzeroRowsAndCols-methods.R'
        'organism-methods.R' 'package.R' 'prepareTemplate.R'
        'rankedMatrix.R' 'reexports-coerce.R' 'reexports.R'
        'sampleData-methods.R' 'sampleNames-methods.R'
        'sanitizeSampleData.R' 'select-methods.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' 'transmit.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 3.6.2; ; 2020-03-17 15:18:03 UTC; unix
