R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.37.0)

IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle

S4-utils.R show-utils.R utils.R normarg-utils.R bindROWS.R
LLint-class.R isSorted.R subsetting-utils.R vector-utils.R
integer-utils.R character-utils.R raw-utils.R eval-utils.R
map_ranges_to_runs.R RectangularData-class.R Annotated-class.R
DataFrame_OR_NULL-class.R Vector-class.R Vector-comparison.R
Vector-setops.R Vector-merge.R Hits-class.R Hits-comparison.R
Hits-setops.R Rle-class.R Rle-utils.R Factor-class.R
List-class.R List-comparison.R splitAsList.R List-utils.R
SimpleList-class.R HitsList-class.R DataFrame-class.R
DataFrame-combine.R DataFrame-comparison.R DataFrame-utils.R
DataFrameFactor-class.R TransposedDataFrame-class.R
Pairs-class.R FilterRules-class.R stack-methods.R
expand-methods.R aggregate-methods.R shiftApply-methods.R zzz.R

Hervé Pagès [aut, cre],
  Michael Lawrence [aut],
  Patrick Aboyoun [aut],
  Aaron Lun [ctb]

S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

R (>= 4.0.0), methods, utils, graphics, stats

Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,
Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2,
flowClust, MSnbase, annotate, RUnit

S3-classes-as-S4-classes.R utils.R normarg-utils.R
replaceSlots.R aperm.R append.R as.data.frame.R as.list.R
as.vector.R cbind.R colSums.R do.call.R duplicated.R eval.R
Extremes.R format.R funprog.R get.R grep.R is.unsorted.R
lapply.R mapply.R match.R mean.R nrow.R order.R paste.R rank.R
rep.R row_colnames.R sets.R sort.R start.R subset.R t.R table.R
tapply.R unique.R unlist.R unsplit.R relist.R var.R which.R
which.min.R boxplot.R image.R density.R IQR.R mad.R residuals.R
weights.R xtabs.R annotation.R combine.R dbconn.R dge.R dims.R
fileName.R normalize.R Ontology.R organism_species.R path.R
plotMA.R plotPCA.R score.R strand.R toTable.R type.R
updateObject.R testPackage.R zzz.R