R/reexports-01-functions.R

## NOTE methods reexports here are used in bcbioRNASeq and pointillism.
## These are safe to remove once downstream packages are updated.

#' @importFrom AcidGenerics CharacterList
#' @export
AcidGenerics::CharacterList

#' @importFrom AcidGenerics DataFrame
#' @export
AcidGenerics::DataFrame

#' @importFrom AcidGenerics DataFrameList
#' @export
AcidGenerics::DataFrameList

#' @importFrom AcidGenomes EntrezGeneInfo
#' @export
AcidGenomes::EntrezGeneInfo

#' @importFrom AcidGenerics FactorList
#' @export
AcidGenerics::FactorList

#' @importFrom pipette GRanges
#' @export
pipette::GRanges

#' @importFrom pipette GRangesList
#' @export
pipette::GRangesList

#' @importFrom AcidGenomes HGNC
#' @export
AcidGenomes::HGNC

#' @importFrom AcidGenomes HGNC2Ensembl
#' @export
AcidGenomes::HGNC2Ensembl

#' @importFrom AcidGenerics IRanges
#' @export
AcidGenerics::IRanges

#' @importFrom AcidGenerics IntegerList
#' @export
AcidGenerics::IntegerList

#' @importFrom AcidGenerics LLint
#' @export
AcidGenerics::LLint

#' @importFrom AcidGenerics List
#' @export
AcidGenerics::List

#' @importFrom AcidGenerics LogicalList
#' @export
AcidGenerics::LogicalList

#' @importFrom pipette Matrix
#' @export
pipette::Matrix

#' @importFrom AcidGenomes MGI2Ensembl
#' @export
AcidGenomes::MGI2Ensembl

#' @importFrom AcidGenerics NumericList
#' @export
AcidGenerics::NumericList

#' @importFrom AcidGenerics Rle
#' @export
AcidGenerics::Rle

#' @importFrom AcidGenerics RleList
#' @export
AcidGenerics::RleList

#' @importFrom AcidGenerics SimpleList
#' @export
AcidGenerics::SimpleList

#' @importFrom AcidSingleCell SingleCellExperiment
#' @export
AcidSingleCell::SingleCellExperiment

#' @importFrom AcidGenerics SplitDataFrameList
#' @export
AcidGenerics::SplitDataFrameList

#' @importFrom AcidExperiment SummarizedExperiment
#' @export
AcidExperiment::SummarizedExperiment

#' @importFrom AcidBase URLencode
#' @export
AcidBase::URLencode

#' @importFrom AcidCLI alert
#' @export
AcidCLI::alert

#' @importFrom AcidCLI alertDanger
#' @export
AcidCLI::alertDanger

#' @importFrom AcidCLI alertInfo
#' @export
AcidCLI::alertInfo

#' @importFrom AcidCLI alertSuccess
#' @export
AcidCLI::alertSuccess

#' @importFrom AcidCLI alertWarning
#' @export
AcidCLI::alertWarning

#' @importFrom AcidGenomes annotable
#' @export
AcidGenomes::annotable

#' @importFrom AcidBase appendToBody
#' @export
AcidBase::appendToBody

#' @importFrom AcidBase arrow
#' @export
AcidBase::arrow

#' @importFrom methods as
#' @export
methods::as

#' @importFrom AcidBase as.formula
#' @export
AcidBase::as.formula

#' @importFrom pipette assignAndSaveData
#' @export
pipette::assignAndSaveData

#' @importFrom AcidBase axisTicks
#' @export
AcidBase::axisTicks

#' @importFrom AcidBase barcodePattern
#' @export
AcidBase::barcodePattern

#' @importFrom AcidBase basenameSansExt
#' @export
AcidBase::basenameSansExt

#' @importFrom pipette cacheURL
#' @export
pipette::cacheURL

#' @importFrom AcidBase capture.output
#' @export
AcidBase::capture.output

#' @importFrom AcidBase classContains
#' @export
AcidBase::classContains

#' @importFrom AcidBase colorRampPalette
#' @export
AcidBase::colorRampPalette

#' @importFrom pipette column_to_rownames
#' @export
pipette::column_to_rownames

#' @importFrom AcidBase compress
#' @export
AcidBase::compress

#' @importFrom AcidBase compressExtPattern
#' @export
AcidBase::compressExtPattern

#' @importFrom AcidGenomes currentEnsemblGenomeBuild
#' @export
AcidGenomes::currentEnsemblGenomeBuild

#' @importFrom AcidGenomes currentEnsemblVersion
#' @export
AcidGenomes::currentEnsemblVersion

#' @importFrom AcidGenomes currentFlyBaseVersion
#' @export
AcidGenomes::currentFlyBaseVersion

#' @importFrom AcidGenomes currentGencodeGenomeBuild
#' @export
AcidGenomes::currentGencodeGenomeBuild

#' @importFrom AcidGenomes currentGencodeVersion
#' @export
AcidGenomes::currentGencodeVersion

#' @importFrom AcidGenomes currentRefSeqGenomeBuild
#' @export
AcidGenomes::currentRefSeqGenomeBuild

#' @importFrom AcidGenomes currentRefSeqVersion
#' @export
AcidGenomes::currentRefSeqVersion

#' @importFrom AcidGenomes currentUCSCGenomeBuild
#' @export
AcidGenomes::currentUCSCGenomeBuild

#' @importFrom AcidGenomes currentWormBaseVersion
#' @export
AcidGenomes::currentWormBaseVersion

#' @importFrom AcidBase data
#' @export
AcidBase::data

#' @importFrom AcidBase decompress
#' @export
AcidBase::decompress

#' @importFrom AcidExperiment detectLanes
#' @export
AcidExperiment::detectLanes

#' @importFrom AcidGenomes detectOrganism
#' @export
AcidGenomes::detectOrganism

#' @importFrom AcidBase dist
#' @export
AcidBase::dist

#' @importFrom AcidCLI dl
#' @export
AcidCLI::dl

#' @importFrom AcidBase dots
#' @export
AcidBase::dots

#' @importFrom AcidBase download
#' @export
AcidBase::download

#' @importFrom AcidGenomes downloadEnsemblGenome
#' @export
AcidGenomes::downloadEnsemblGenome

#' @importFrom AcidGenomes downloadGencodeGenome
#' @export
AcidGenomes::downloadGencodeGenome

#' @importFrom AcidGenomes downloadRefSeqGenome
#' @export
AcidGenomes::downloadRefSeqGenome

#' @importFrom AcidGenomes downloadUCSCGenome
#' @export
AcidGenomes::downloadUCSCGenome

#' @importFrom AcidBase ecdf
#' @export
AcidBase::ecdf

#' @importFrom AcidGenomes emptyRanges
#' @export
AcidGenomes::emptyRanges

#' @importFrom AcidBase extPattern
#' @export
AcidBase::extPattern

#' @importFrom AcidBase fileDepth
#' @export
AcidBase::fileDepth

#' @importFrom AcidBase fileExt
#' @export
AcidBase::fileExt

#' @importFrom AcidBase forceDetach
#' @export
AcidBase::forceDetach

#' @importFrom methods formalArgs
#' @export
methods::formalArgs

#' @importFrom AcidBase formalsList
#' @export
AcidBase::formalsList

#' @importFrom AcidBase formula
#' @export
AcidBase::formula

#' @importFrom AcidGenomes geneSynonyms
#' @export
AcidGenomes::geneSynonyms

#' @importFrom AcidBase genomeMetadataNames
#' @export
AcidBase::genomeMetadataNames

#' @importFrom AcidBase getS3method
#' @export
AcidBase::getS3method

#' @importFrom pipette getURL
#' @export
pipette::getURL

#' @importFrom pipette getURLDirList
#' @export
pipette::getURLDirList

#' @importFrom AcidCLI h1
#' @export
AcidCLI::h1

#' @importFrom AcidCLI h2
#' @export
AcidCLI::h2

#' @importFrom AcidCLI h3
#' @export
AcidCLI::h3

#' @importFrom AcidCLI h4
#' @export
AcidCLI::h4

#' @importFrom AcidCLI h5
#' @export
AcidCLI::h5

#' @importFrom AcidCLI h6
#' @export
AcidCLI::h6

#' @importFrom AcidCLI h7
#' @export
AcidCLI::h7

#' @importFrom AcidBase hclust
#' @export
AcidBase::hclust

#' @importFrom pipette import
#' @export
pipette::import

#' @importFrom AcidExperiment importSampleData
#' @export
AcidExperiment::importSampleData

#' @importFrom AcidGenomes importTx2Gene
#' @export
AcidGenomes::importTx2Gene

#' @importFrom AcidBase initDir
#' @export
AcidBase::initDir

#' @importFrom methods is
#' @export
methods::is

#' @importFrom AcidBase lanePattern
#' @export
AcidBase::lanePattern

#' @importFrom pipette loadData
#' @export
pipette::loadData

#' @importFrom pipette loadDataAsName
#' @export
pipette::loadDataAsName

#' @importFrom pipette loadRemoteData
#' @export
pipette::loadRemoteData

#' @importFrom pipette localOrRemoteFile
#' @export
pipette::localOrRemoteFile

#' @importFrom AcidGenomes makeGRangesFromEnsDb
#' @export
AcidGenomes::makeGRangesFromEnsDb

#' @importFrom AcidGenomes makeGRangesFromEnsembl
#' @export
AcidGenomes::makeGRangesFromEnsembl

#' @importFrom AcidGenomes makeGRangesFromGFF
#' @export
AcidGenomes::makeGRangesFromGFF

#' @importFrom AcidGenomes makeGene2SymbolFromEnsDb
#' @export
AcidGenomes::makeGene2SymbolFromEnsDb

#' @importFrom AcidGenomes makeGene2SymbolFromEnsembl
#' @export
AcidGenomes::makeGene2SymbolFromEnsembl

#' @importFrom AcidGenomes makeGene2SymbolFromGFF
#' @export
AcidGenomes::makeGene2SymbolFromGFF

#' @importFrom AcidGenomes makeProtein2GeneFromEnsembl
#' @export
AcidGenomes::makeProtein2GeneFromEnsembl

#' @importFrom AcidSingleCell makeSingleCellExperiment
#' @export
AcidSingleCell::makeSingleCellExperiment

#' @importFrom AcidExperiment makeSummarizedExperiment
#' @export
AcidExperiment::makeSummarizedExperiment

#' @importFrom AcidGenomes makeTx2GeneFromEnsDb
#' @export
AcidGenomes::makeTx2GeneFromEnsDb

#' @importFrom AcidGenomes makeTx2GeneFromEnsembl
#' @export
AcidGenomes::makeTx2GeneFromEnsembl

#' @importFrom AcidGenomes makeTx2GeneFromFASTA
#' @export
AcidGenomes::makeTx2GeneFromFASTA

#' @importFrom AcidGenomes makeTx2GeneFromGFF
#' @export
AcidGenomes::makeTx2GeneFromGFF

#' @importFrom AcidBase majorVersion
#' @export
AcidBase::majorVersion

#' @importFrom AcidSingleCell mapCellsToSamples
#' @export
AcidSingleCell::mapCellsToSamples

#' @importFrom AcidGenomes mapEnsemblBuildToUCSC
#' @export
AcidGenomes::mapEnsemblBuildToUCSC

#' @importFrom AcidGenomes mapEnsemblReleaseToURL
#' @export
AcidGenomes::mapEnsemblReleaseToURL

#' @importFrom AcidGenomes mapHumanOrthologs
#' @export
AcidGenomes::mapHumanOrthologs

#' @importFrom AcidGenomes mapUCSCBuildToEnsembl
#' @export
AcidGenomes::mapUCSCBuildToEnsembl

#' @importFrom AcidMarkdown markdownHeader
#' @export
AcidMarkdown::markdownHeader

#' @importFrom AcidMarkdown markdownLink
#' @export
AcidMarkdown::markdownLink

#' @importFrom AcidMarkdown markdownList
#' @export
AcidMarkdown::markdownList

#' @importFrom AcidMarkdown markdownPlots
#' @export
AcidMarkdown::markdownPlots

#' @importFrom AcidMarkdown markdownTables
#' @export
AcidMarkdown::markdownTables

#' @importFrom AcidExperiment matchInterestingGroups
#' @export
AcidExperiment::matchInterestingGroups

#' @importFrom AcidExperiment matchesGene2Symbol
#' @export
AcidExperiment::matchesGene2Symbol

#' @importFrom AcidExperiment matchesInterestingGroups
#' @export
AcidExperiment::matchesInterestingGroups

#' @importFrom AcidMarkdown mdHeader
#' @export
AcidMarkdown::mdHeader

#' @importFrom AcidMarkdown mdLink
#' @export
AcidMarkdown::mdLink

#' @importFrom AcidMarkdown mdList
#' @export
AcidMarkdown::mdList

#' @importFrom AcidMarkdown mdPlots
#' @export
AcidMarkdown::mdPlots

#' @importFrom AcidMarkdown mdTables
#' @export
AcidMarkdown::mdTables

#' @importFrom AcidBase metadataDenylist
#' @export
AcidBase::metadataDenylist

#' @importFrom AcidBase methodFormals
#' @export
AcidBase::methodFormals

#' @importFrom AcidBase methodFunction
#' @export
AcidBase::methodFunction

#' @importFrom AcidBase metricsCols
#' @export
AcidBase::metricsCols

#' @importFrom AcidExperiment microplate
#' @export
AcidExperiment::microplate

#' @importFrom AcidExperiment minimalSampleData
#' @export
AcidExperiment::minimalSampleData

#' @importFrom AcidBase minorVersion
#' @export
AcidBase::minorVersion

#' @importFrom AcidBase model.matrix
#' @export
AcidBase::model.matrix

#' @importFrom pipette naStrings
#' @export
pipette::naStrings

#' @importFrom methods new
#' @export
methods::new

#' @importFrom AcidCLI ol
#' @export
AcidCLI::ol

#' @importFrom AcidBase packageName
#' @export
AcidBase::packageName

#' @importFrom AcidBase packageVersion
#' @export
AcidBase::packageVersion

#' @importFrom AcidBase pasteURL
#' @export
AcidBase::pasteURL

#' @importFrom AcidBase prcomp
#' @export
AcidBase::prcomp

#' @importFrom AcidMarkdown prepareTemplate
#' @export
AcidMarkdown::prepareTemplate

#' @importFrom AcidBase printString
#' @export
AcidBase::printString

#' @importFrom pipette rbindlist
#' @export
pipette::rbindlist

#' @importFrom AcidBase realpath
#' @export
AcidBase::realpath

#' @importFrom AcidBase relevel
#' @export
AcidBase::relevel

#' @importFrom AcidBase reorder
#' @export
AcidBase::reorder

#' @importFrom AcidBase requireNamespaces
#' @export
AcidBase::requireNamespaces

#' @importFrom AcidBase rgb
#' @export
AcidBase::rgb

#' @importFrom pipette rownames_to_column
#' @export
pipette::rownames_to_column

#' @importFrom AcidExperiment sanitizeSampleData
#' @export
AcidExperiment::sanitizeSampleData

#' @importFrom AcidBase sanitizeVersion
#' @export
AcidBase::sanitizeVersion

#' @importFrom pipette saveData
#' @export
pipette::saveData

#' @importFrom AcidCLI separator
#' @export
AcidCLI::separator

#' @importFrom AcidExperiment session_info
#' @export
AcidExperiment::session_info

#' @importFrom AcidBase sessionInfo
#' @export
AcidBase::sessionInfo

#' @importFrom AcidGenerics setdiff
#' @export
AcidGenerics::setdiff

#' @importFrom AcidBase shell
#' @export
AcidBase::shell

#' @importFrom AcidBase showSlotInfo
#' @export
AcidBase::showSlotInfo

#' @importFrom pipette sparseMatrix
#' @export
pipette::sparseMatrix

#' @importFrom AcidBase standardizeCall
#' @export
AcidBase::standardizeCall

#' @importFrom stringr str_detect
#' @export
stringr::str_detect

#' @importFrom stringr str_dup
#' @export
stringr::str_dup

#' @importFrom stringr str_extract
#' @export
stringr::str_extract

#' @importFrom stringr str_extract_all
#' @export
stringr::str_extract_all

#' @importFrom stringr str_length
#' @export
stringr::str_length

#' @importFrom stringr str_locate_all
#' @export
stringr::str_locate_all

#' @importFrom stringr str_match
#' @export
stringr::str_match

#' @importFrom stringr str_match_all
#' @export
stringr::str_match_all

#' @importFrom stringr str_pad
#' @export
stringr::str_pad

#' @importFrom stringr str_replace
#' @export
stringr::str_replace

#' @importFrom stringr str_replace_all
#' @export
stringr::str_replace_all

#' @importFrom stringr str_replace_na
#' @export
stringr::str_replace_na

#' @importFrom stringr str_split
#' @export
stringr::str_split

#' @importFrom stringr str_split_fixed
#' @export
stringr::str_split_fixed

#' @importFrom stringr str_sub
#' @export
stringr::str_sub

#' @importFrom stringr str_subset
#' @export
stringr::str_subset

## Consider including these:
## - str_to_lower
## - str_to_sentence
## - str_to_title
## - str_to_upper

#' @importFrom stringr str_trunc
#' @export
stringr::str_trunc

#' @importFrom pipette tibble
#' @export
pipette::tibble

#' @importFrom AcidCLI toInlineString
#' @export
AcidCLI::toInlineString

#' @importFrom pipette transmit
#' @export
pipette::transmit

#' @importFrom AcidCLI txt
#' @export
AcidCLI::txt

#' @importFrom AcidCLI ul
#' @export
AcidCLI::ul

#' @importFrom AcidBase unit
#' @export
AcidBase::unit

#' @importFrom AcidBase untar
#' @export
AcidBase::untar

#' @importFrom AcidBase updateMessage
#' @export
AcidBase::updateMessage

#' @importFrom methods validObject
#' @export
methods::validObject

#' @importFrom AcidCLI verbatim
#' @export
AcidCLI::verbatim
acidgenomics/basejump documentation built on June 21, 2021, 9:43 a.m.