annotation              Accessing annotation information
aperm                   Transposing an array-like object
append                  Append elements to a vector-like object
as.data.frame           Coerce to a data frame
as.list                 Coerce to a list
as.vector               Coerce an object into a vector
BiocGenerics-package    S4 generic functions for Bioconductor
boxplot                 Box plots
cbind                   Combine objects by rows or columns
combine                 Combining or merging different Bioconductor
                        data structures
containsOutOfMemoryData
                        Does an object contain out-of-memory data?
data                    Data Sets
dbconn                  Accessing SQLite DB information
density                 Kernel density estimation
dge                     Accessors and generic functions used in the
                        context of count datasets
dims                    Get the dimensions of each element of a
                        list-like object
do.call                 Execute a function call
duplicated              Determine duplicate elements
eval                    Evaluate an (unevaluated) expression
evalq                   Evaluate an (unevaluated) expression
Extremes                Maxima and minima
fileName                Accessing the file name of an object
format                  Format an R object for pretty printing
funprog                 Common higher-order functions in functional
                        programming languages
get                     Return the value of a named object
grep                    Pattern Matching and Replacement
image                   Display a color image
IQR                     The Interquartile Range
is.unsorted             Test if a vector-like object is not sorted
lapply                  Apply a function over a list-like or
                        vector-like object
longForm                Turn object into long form
mad                     Median Absolute Deviation
mapply                  Apply a function to multiple list-like or
                        vector-like arguments
match                   Value matching
mean                    Arithmetic Mean
normalize               Normalize an object
nrow                    The number of rows/columns of an array-like
                        object
Ontology                Generic Ontology getter
order                   Ordering permutation
organism_species        Organism and species accessors
paste                   Concatenate strings
paste2                  Concatenate strings (binary form)
path                    Accessing the path of an object
plotMA                  MA-plot: plot differences versus averages for
                        high-throughput data
plotPCA                 PCA-plot: Principal Component Analysis plot
rank                    Ranks the values in a vector-like object
relist                  Re-listing an unlist()ed object
rep.int                 Replicate elements of a vector-like object
residuals               Extract model residuals
rotate                  Rotate an object
row+colnames            Row and column names
S3-classes-as-S4-classes
                        S3 classes as S4 classes
saveRDS                 The saveRDS() S4 generic and default method
scale                   Scaling and centering of matrix-like objects
score                   Score accessor
sequence                Create a vector of sequences
setops                  Set operations
sort                    Sorting a vector-like object
start                   The start(), end(), width(), and pos() generic
                        getters and setters
strand                  Accessing strand information
subset                  Subsetting vector-like, matrix-like and
                        data-frame-like objects
t                       Matrix Transpose
table                   Cross tabulation and table creation
tapply                  Apply a function over a ragged array
testPackage             Run RUnit package unit tests
toTable                 An alternative to as.data.frame()
transform               Transform an object
type                    Accessing the type of an object
unique                  Extract unique elements
unlist                  Flatten list-like objects
unsplit                 Unsplit a list-like object
updateObject            Update an object to its current class
                        definition
var                     Variance and Standard Deviation
weights                 Extract model weights
which                   Which values in an object are considered TRUE?
which.min               What's the index of the first min or max value
                        in an object?
xtabs                   Cross tabulation
