BiocGenerics-package	BiocGenerics-package
%in%	match
add_prefix	paste2
add_suffix	paste2
annotation	annotation
annotation<-	annotation
anyDuplicated	duplicated
aperm	aperm
append	append
as.data.frame	as.data.frame
as.list	as.list
as.vector	as.vector
AsIs-class	S3-classes-as-S4-classes
basename	path
basename,ANY-method	path
basename<-	path
basename<-,ANY-method	path
basename<-,character-method	path
BiocGenerics	BiocGenerics-package
boxplot	boxplot
bzfile-class	S3-classes-as-S4-classes
cbind	cbind
character_OR_connection-class	S3-classes-as-S4-classes
class:OutOfMemoryObject	containsOutOfMemoryData
colnames	row_colnames
colnames<-	row_colnames
combine	combine
combine,ANY,missing-method	combine
combine,data.frame,data.frame-method	combine
combine,matrix,matrix-method	combine
conditions	dge
conditions<-	dge
connection-class	S3-classes-as-S4-classes
containsOutOfMemoryData	containsOutOfMemoryData
containsOutOfMemoryData,ANY-method	containsOutOfMemoryData
containsOutOfMemoryData,environment-method	containsOutOfMemoryData
containsOutOfMemoryData,list-method	containsOutOfMemoryData
containsOutOfMemoryData,OutOfMemoryObject-method	containsOutOfMemoryData
counts	dge
counts<-	dge
dbconn	dbconn
dbfile	dbconn
density	density
design	dge
design<-	dge
dge	dge
dims	dims
dirname	path
dirname,ANY-method	path
dirname<-	path
dirname<-,ANY-method	path
dirname<-,character-method	path
dispTable	dge
dispTable<-	dge
dist-class	S3-classes-as-S4-classes
do.call	do.call
duplicated	duplicated
end	start
end<-	start
estimateDispersions	dge
estimateSizeFactors	dge
eval	eval
evalq	evalq
Extremes	Extremes
fifo-class	S3-classes-as-S4-classes
file-class	S3-classes-as-S4-classes
fileName	fileName
Filter	funprog
Find	funprog
format	format
format.list	format
funprog	funprog
get	get
getObjectSlots	updateObject
grep	grep
grepl	grep
gzcon-class	S3-classes-as-S4-classes
gzfile-class	S3-classes-as-S4-classes
image	image
intersect	setops
invertStrand	strand
invertStrand,ANY-method	strand
IQR	IQR
is.unsorted	is.unsorted
lapply	lapply
longForm	longForm
mad	mad
Map	funprog
mapply	mapply
match	match
mean	mean
mget	get
NCOL	nrow
ncol	nrow
ncols	dims
normalize	normalize
NROW	nrow
nrow	nrow
nrows	dims
Ontology	Ontology
order	order
organism	organism_species
organism<-	organism_species
organism_species	organism_species
OutOfMemoryObject	containsOutOfMemoryData
OutOfMemoryObject-class	containsOutOfMemoryData
paste	paste
paste2	paste2
paste2,ANY,ANY-method	paste2
paste2,ANY,array-method	paste2
paste2,array,ANY-method	paste2
paste2,array,array-method	paste2
path	path
path<-	path
pipe-class	S3-classes-as-S4-classes
plotDispEsts	dge
plotMA	plotMA
plotMA,ANY-method	plotMA
plotPCA	plotPCA
pmax	Extremes
pmax.int	Extremes
pmin	Extremes
pmin.int	Extremes
pos	start
Position	funprog
rank	rank
rbind	cbind
Reduce	funprog
relist	relist
rep.int	rep
residuals	residuals
row+colnames	row_colnames
rownames	row_colnames
rownames<-	row_colnames
S3-classes-as-S4-classes	S3-classes-as-S4-classes
sapply	lapply
saveRDS	saveRDS
saveRDS,ANY-method	saveRDS
score	score
score<-	score
sd	var
setdiff	setops
setequal	setops
setops	setops
sets	setops
sizeFactors	dge
sizeFactors<-	dge
sockconn-class	S3-classes-as-S4-classes
sort	sort
species	organism_species
species<-	organism_species
start	start
start<-	start
strand	strand
strand<-	strand
subset	subset
t	t
table	table
tapply	tapply
terminal-class	S3-classes-as-S4-classes
testPackage	testPackage
textConnection-class	S3-classes-as-S4-classes
toTable	toTable
type	type
type,array-method	type
type,data.frame-method	type
type,factor-method	type
type,vector-method	type
type<-	type
type<-,array-method	type
type<-,vector-method	type
union	setops
unique	unique
unlist	unlist
unsplit	unsplit
unstrand	strand
unz-class	S3-classes-as-S4-classes
updateObject	updateObject
updateObject,ANY-method	updateObject
updateObject,environment-method	updateObject
updateObject,envRefClass-method	updateObject
updateObject,formula-method	updateObject
updateObjectFromSlots	updateObject
url-class	S3-classes-as-S4-classes
var	var
weights	weights
which	which
which.max	which.min
which.min	which.min
width	start
width<-	start
xtabs	xtabs
