AA_TABLE	AA_TABLE
AA_TABLE_REVERSED	AA_TABLE
add.pb	set.pb
apply.asymm	apply.symm
apply.symm	apply.symm
assymetry	assymetry
barcodes.to.reads	barcodes.to.reads
beta.prob	beta.prob
bootstrap.tcr	bootstrap.tcr
bunch.translate	revcomp
chao1	inverse.simpson
check.distribution	check.distribution
clonal.proportion	tailbound.proportion
clonal.space.homeostasis	clonal.space.homeostasis
cloneset.stats	cloneset.stats
clonotypescount	get.inframes
codon.variants	codon.variants
column.summary	column.summary
contamination.stats	contamination.stats
convergence.index	convergence.index
cosine.sharing	cosine.sharing
cosine.similarity	cosine.similarity
count.frames	get.inframes
count.inframes	get.inframes
count.outframes	get.inframes
decontamination	contamination.stats
diversity	inverse.simpson
downsample	resample
entropy	entropy
entropy.seg	entropy.seg
exact.match	find.similar.sequences
find.clonotypes	find.clonotypes
find.similar.sequences	find.similar.sequences
fix.alleles	fix.alleles
fix.genes	fix.alleles
gc.content	gc.content
genealphabets	segments.alphabets
generate.kmers	generate.kmers
generate.kmers.prob	generate.kmers
generate.tcr	generate.tcr
genesegments	segments.list
geneUsage	geneUsage
get.all.substrings	get.all.substrings
get.deletions.alpha	get.deletions.alpha
get.deletions.beta	get.deletions.alpha
get.frames	get.inframes
get.group.names	set.group.vector
get.inframes	get.inframes
get.kmer.column	kmer.table
get.kmers	get.kmers
get.outframes	get.inframes
get.people.names	set.people.vector
gibbs.sampler	gibbs.sampler
gini	inverse.simpson
gini.simpson	inverse.simpson
group.clonotypes	group.clonotypes
hamming.match	find.similar.sequences
has.class	has.class
horn.index	cosine.similarity
HUMAN_IGHD	segments.alphabets
HUMAN_IGHJ	segments.alphabets
HUMAN_IGHV	segments.alphabets
HUMAN_IGKJ	segments.alphabets
HUMAN_IGKV	segments.alphabets
HUMAN_IGLJ	segments.alphabets
HUMAN_IGLV	segments.alphabets
HUMAN_TRAJ	segments.alphabets
HUMAN_TRAV	segments.alphabets
HUMAN_TRBD	segments.alphabets
HUMAN_TRBJ	segments.alphabets
HUMAN_TRBV	segments.alphabets
HUMAN_TRBV_ALS	segments.alphabets
HUMAN_TRBV_FAM	segments.alphabets
HUMAN_TRBV_GEN	segments.alphabets
HUMAN_TRBV_MITCR	segments.alphabets
HUMAN_TRDD	segments.alphabets
HUMAN_TRDJ	segments.alphabets
HUMAN_TRDV	segments.alphabets
HUMAN_TRGJ	segments.alphabets
HUMAN_TRGV	segments.alphabets
insertion.stats	column.summary
intersectClonesets	intersectClonesets
intersectCount	intersectClonesets
intersectIndices	intersectClonesets
intersectLogic	intersectClonesets
inverse.simpson	inverse.simpson
jaccard.index	cosine.similarity
js.div	entropy
js.div.seg	entropy.seg
kl.div	entropy
kmer.profile	kmer.profile
kmer.table	kmer.table
kmers.profile	kmer.profile
levenshtein.match	find.similar.sequences
loglikelihood	loglikelihood
MACMUL_TRBJ	segments.alphabets
MACMUL_TRBV	segments.alphabets
matrixdiagcopy	matrixdiagcopy
matrixSubgroups	matrixSubgroups
morisitas.index	cosine.similarity
MOUSE_IGHD	segments.alphabets
MOUSE_IGHJ	segments.alphabets
MOUSE_IGHV	segments.alphabets
MOUSE_IGKJ	segments.alphabets
MOUSE_IGKV	segments.alphabets
MOUSE_IGLJ	segments.alphabets
MOUSE_IGLV	segments.alphabets
MOUSE_TRAJ	segments.alphabets
MOUSE_TRAV	segments.alphabets
MOUSE_TRBJ	segments.alphabets
MOUSE_TRBV	segments.alphabets
MOUSE_TRDD	segments.alphabets
MOUSE_TRDJ	segments.alphabets
MOUSE_TRDV	segments.alphabets
MOUSE_TRGJ	segments.alphabets
MOUSE_TRGV	segments.alphabets
mutated.neighbours	mutated.neighbours
mutation.network	mutation.network
overlap.coef	cosine.similarity
ozScore	ozScore
parse.cloneset	parse.cloneset
parse.file	parse.folder
parse.file.list	parse.folder
parse.folder	parse.folder
parse.immunoseq	parse.folder
parse.immunoseq2	parse.folder
parse.immunoseq3	parse.folder
parse.imseq	parse.folder
parse.migec	parse.folder
parse.migmap	parse.folder
parse.mitcr	parse.folder
parse.mitcrbc	parse.folder
parse.mixcr	parse.folder
parse.tcr	parse.folder
parse.vdjtools	parse.folder
pca.segments	pca.segments
pca.segments.2D	pca.segments
pca2euclid	pca2euclid
permutDistTest	permutDistTest
permutedf	permutedf
rarefaction	rarefaction
repDiversity	repDiversity
repLoad	repLoad
repOverlap	repOverlap
repSave	repSave
repseq.stats	cloneset.stats
resample	resample
revcomp	revcomp
reverse.string	reverse.string
reverse.translation	codon.variants
sample.clones	sample.clones
sample2D	sample2D
segments.alphabets	segments.alphabets
segments.list	segments.list
set.group.vector	set.group.vector
set.index	set.rank
set.pb	set.pb
set.people.vector	set.people.vector
set.rank	set.rank
shared.clones.count	cosine.sharing
shared.matrix	shared.repertoire
shared.repertoire	shared.repertoire
shared.representation	cosine.sharing
shared.summary	cosine.sharing
similarity	cosine.similarity
slice.fun	top.fun
spectratyping	spectratyping
startmitcr	startmitcr
tailbound.proportion	tailbound.proportion
top.cross	top.cross
top.cross.plot	top.cross
top.cross.vec	top.cross
top.fun	top.fun
top.proportion	tailbound.proportion
translated.nucl.sequences	codon.variants
tversky.index	cosine.similarity
twa	twinsdata
twb	twinsdata
twinsdata	twinsdata
unpermutedf	permutedf
vis.clonal.dynamics	vis.clonal.dynamics
vis.clonal.space	vis.clonal.space
vis.count.len	vis.count.len
vis.gene.usage	vis.gene.usage
vis.group.boxplot	vis.group.boxplot
vis.heatmap	vis.heatmap
vis.J.usage	vis.gene.usage
vis.kmer.histogram	vis.kmer.histogram
vis.logo	vis.logo
vis.number.count	vis.number.count
vis.pca	vis.pca
vis.radarlike	vis.radarlike
vis.rarefaction	vis.rarefaction
vis.shared.clonotypes	vis.shared.clonotypes
vis.top.proportions	vis.top.proportions
vis.V.usage	vis.gene.usage
