Package: basejump
Title: Base Functions for Bioinformatics
Description: Toolkit for bioinformatics and R package development.
Version: 0.12.14
Date: 2020-09-14
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: AnnotationHub, Biobase, BiocGenerics, BiocParallel,
        Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges,
        IRanges, Matrix (>= 1.2), S4Vectors, SingleCellExperiment,
        SummarizedExperiment, acidbase (>= 0.1.14), acidgenerics (>=
        0.3.11), cli (>= 2.0), ensembldb, goalie (>= 0.4.8), magrittr
        (>= 1.5), matrixStats (>= 0.56), methods, pipette (>= 0.4.13),
        scales (>= 1.1), sessioninfo (>= 1.1), stringr (>= 1.4),
        syntactic (>= 0.4.2), tibble (>= 3.0), utils
Suggests: BiocStyle, EnsDb.Hsapiens.v75, RCurl, acidtest (>= 0.3.2),
        biomaRt, datasets, knitr, rmarkdown, testthat
Remotes: acidgenomics/acidbase, acidgenomics/acidgenerics,
        acidgenomics/acidtest, acidgenomics/goalie,
        acidgenomics/pipette, acidgenomics/syntactic
biocViews: DataImport, GenomeAnnotation, Preprocessing
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
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' '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'
        'intersectAll-methods.R' 'intersectionMatrix-methods.R'
        'join-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' 'splitByLevel-methods.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 4.0.2; ; 2020-09-15 01:14:00 UTC; unix
