#Generated by codetoolsBioC version 0.1-0
#Timestamp: Tue Mar 28 11:14:08 2017

#Depends: .GlobalEnv

export(basecallQC)
export(createBCLcommand)
export(createBasemasks)
export(demuxBarplot)
export(demuxBoxplot)
export(indexlengths.bcl2fastqparams)
export(makeFQTable)
export(passFilterBar)
export(passFilterBoxplot)
export(passFilterTilePlot)
export(readlengths.bcl2fastqparams)
export(reportBCL)
export(BCL2FastQparams)
export(summaryConvStatsTable)
export(summaryDemuxTable)
export(validateBCLSheet)
export(baseCallMetrics)
export(demultiplexMetrics)
export(interOpsReport)
exportClasses(BCL2FastQparams)
exportClasses(basecallQC)
exportMethods(indexlengths)
exportMethods(readlengths)

#Imports: data.table, dplyr, DT, ggplot2, IRanges, knitr, lazyeval, magrittr, methods, raster, rmarkdown,
#         Rsamtools, S4Vectors, ShortRead, stats, stringr, tidyr, utils, XML
import(knitr)

import(rmarkdown)

import(yaml)

import(prettydoc)

importClassesFrom(methods, character, data.frame, list)

importMethodsFrom(raster, as.data.frame, as.list, nrow, unique)

importMethodsFrom(ShortRead, lapply, rbind, report, sapply, qa)

importMethodsFrom(XML, xmlToDataFrame)

importFrom(data.table, fread)

importFrom(dplyr, count, everything, filter, group_by, group_by_, mutate, mutate_all, rename, select,
           summarise, summarise_, tbl_df)

importFrom(ggplot2, aes, aes_string, coord_flip, facet_grid, geom_bar, geom_jitter, geom_tile, geom_violin,
           ggplot, scale_fill_gradient2, theme_bw)

importFrom(knitr, kable)

importFrom(lazyeval, interp)

importFrom(magrittr, "%>%")

importFrom(methods, new)

importFrom(raster, readIniFile, validNames)

importFrom(rmarkdown, render)

importFrom(stats, setNames)

importFrom(stringr, str_c, str_dup, str_length, str_replace, str_sub, str_trim, str_to_upper)

importFrom(tidyr, gather, gather_, spread_)

importFrom(utils, write.table)

importFrom(XML, xmlAttrs, xmlName, xmlParse, xmlRoot, xmlTreeParse, xmlValue)

importFrom(DT, datatable)

importFrom(ShortRead, rbind)
