BiocGenerics-package	BiocGenerics-package
annotation	annotation
annotation<-	annotation
anyDuplicated	duplicated
append	append
as.data.frame	as.data.frame
as.vector	as.vector
AsIs-class	S3-classes-as-S4-classes
BiocGenerics	BiocGenerics-package
boxplot	boxplot
bzfile-class	S3-classes-as-S4-classes
cbind	cbind
characterORconnection-class	S3-classes-as-S4-classes
clusterApply	clusterApply
clusterApplyLB	clusterApply
clusterCall	clusterApply
clusterEvalQ	clusterApply
clusterExport	clusterApply
clusterMap	clusterApply
clusterSplit	clusterApply
colMeans	matrix-summary
colnames	row_colnames
colnames<-	row_colnames
colSums	matrix-summary
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
counts	dge
counts<-	dge
dbconn	dbconn
dbfile	dbconn
density	density
design	dge
design<-	dge
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
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	sets
invertStrand	strand
invertStrand,ANY-method	strand
IQR	IQR
is.unsorted	is.unsorted
lapply	lapply
lengths	lengths
mad	mad
Map	funprog
mapply	mapply
match	match
mean	mean
mget	get
NCOL	nrow
ncol	nrow
normalize	normalize
NROW	nrow
nrow	nrow
Ontology	Ontology
order	order
organism	organism_species
organism<-	organism_species
organism_species	organism_species
parApply	clusterApply
parCapply	clusterApply
parLapply	clusterApply
parLapplyLB	clusterApply
parRapply	clusterApply
parSapply	clusterApply
parSapplyLB	clusterApply
paste	paste
pipe-class	S3-classes-as-S4-classes
plotDispEsts	dge
plotMA	plotMA
plotMA,ANY-method	plotMA
plotPCA	plotPCA
plotPCA,ANY-method	plotPCA
pmax	Extremes
pmax.int	Extremes
pmin	Extremes
pmin.int	Extremes
Position	funprog
rank	rank
rbind	cbind
Reduce	funprog
relist	relist
rep.int	rep
residuals	residuals
row+colnames	row_colnames
rowMeans	matrix-summary
rownames	row_colnames
rownames<-	row_colnames
rowSums	matrix-summary
S3-classes-as-S4-classes	S3-classes-as-S4-classes
sapply	lapply
score	score
score<-	score
sd	var
setdiff	sets
sets	sets
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
union	sets
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
updateObject,list-method	updateObject
updateObjectFromSlots	updateObject
url-class	S3-classes-as-S4-classes
var	var
weights	weights
which	which
which.max	which
which.min	which
width	start
width<-	start
xtabs	xtabs
