R/BASiCS_Package.R

In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

#' @useDynLib BASiCS
#' @importFrom coda HPDinterval mcmc effectiveSize
#' @importFrom cowplot plot_grid
#' @importFrom ggplot2 ggplot aes .data
#' @importFrom ggplot2 geom_ribbon geom_segment geom_boxplot geom_hex geom_col
#'                     geom_hline geom_line geom_point geom_histogram
#'                     geom_violin geom_vline
#' @importFrom ggplot2 scale_fill_gradientn scale_x_log10 scale_y_log10 
#'                     scale_x_continuous scale_y_continuous scale_colour_manual
#'                     scale_fill_brewer scale_colour_brewer scale_color_brewer
#' @importFrom ggplot2 theme_minimal theme_classic theme_bw theme
#'                      element_blank
#' @importFrom ggplot2 xlab ylab labs ggtitle xlim ylim
#' @importFrom ggplot2 after_stat
#' @importFrom grDevices adjustcolor colorRampPalette nclass.FD
#' @importFrom ggExtra ggMarginal
#' @importFrom graphics segments
#' @importFrom MASS mvrnorm
#' @importFrom matrixStats colMeans2 colMedians colVars
#' @importFrom matrixStats rowMeans2 rowMedians rowVars   
#' @importFrom methods .hasSlot is new show slotNames Summary 
#' @importFrom Rcpp evalCpp sourceCpp
#' @importFrom S4Vectors DataFrame
#' @importFrom scran calculateSumFactors
#' @importFrom scuttle cleanSizeFactors
#' @importFrom stats acf median model.matrix rgamma rpois runif var lm lag
#'  quantile rlnorm density
#' @importFrom SingleCellExperiment SingleCellExperiment counts 
#' @importFrom SingleCellExperiment altExp altExp<- 
#' @importFrom SingleCellExperiment altExpNames altExpNames<-
#' @importFrom stats4 plot
#' @importFrom SummarizedExperiment SummarizedExperiment assay assays assayNames
#' @importFrom SummarizedExperiment colData colData<- rowData rowData<-
#' @importFrom viridis scale_color_viridis scale_fill_viridis 
#' @importFrom hexbin hexbin
#' @importFrom utils packageVersion read.delim write.table write.table
#' @importFrom assertthat assert_that
#' @importFrom posterior rhat
#' @importMethodsFrom BiocGenerics counts colnames rownames subset updateObject 
#' @importMethodsFrom Matrix t rowMeans
#' @importClassesFrom Biobase Versioned
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