ABT
ADT
AE
AIRR
AUCell
Andreatta
Atchley
Autoencoder
Autoencoders
BCR
BCRs
BD
BIOCARTA
BLOSUM
BPPARAM
Barcode
Barcodes
BioC
Bioc
BiocParallel
Biotechnologies
Bormann
CAERGSGGSYIPTF
CARKVRDSSYKLIF
CASSDPSGRQGPRWDTQYF
CASSDSGYNEQFF
CASSVRRERANTGELFF
CDR
CDRs
CGN
CGP
CMD
CNNs
COVID
CTaa
CTstrict
CVVSDNTGGFKTIF
Carmona
ChangeLog
Chao
ClonalDiversity
CoNGA
Codecov
CombineBCR
CombineExpression
Commun
Complementarity
Contig
Contigs
Convolutional
Corvino
Cruciani
DESeq
Damerau
Deconvolute
Dgene
Directionality
Downsampling
Drs
FASGAI
FASTA
FWR
FWRs
FilteringMulti
Florian
Francesco
GEX
GIANA
GSE
GSEA
GSEABase
GSVA
GeneSetCollection
Genomics’
Germline
Gini
Github
HEL
HTO
Hyperexpanded
Hypermutation
IGH
IGHD
IGHJ
IGHM
IGK
IGKJ
IGL
IMGT
IMMUNESIGDB
Ig
IgA
IgBLAST
IgD
IgG
IgM
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Immunarch
Inv
JC
JS
Jaccard
Jgene
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Lagattuta
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Liangtao
Lysozyme
MAIT
MSWHIM
MSigDB
Massimo
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McPAS
MiXCR
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Morisita's
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NES
NG
Nebulosa
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Nicky
Nikolaj
Noonan
OHE
Oligo
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PIRD
PLZF
PLoS
PMID
PWM
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ParseBio
Physicochemical
Pielou
Pielou's
ProjectTIL
ProtFP
Readded
Rebasing
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SCE
SHM
SRA
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SampleType
Satija's
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SingleCellExperiment
Startrac
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TCR
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Vgene
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Visualise
Visualising
VizGene
Voigt
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WAT
WNN
Walktrap
Waterman
Wunsch
Yu
Zenodo
Zhang
Zheng
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abT
abundanceContig
addVariable
adjacencyMatrix
airr
al
alakazam
alluvialClones
alluvialClonotype
alluvialClonotypes
annotateInvariant
assertthat
asy
atchleyFactors
autoencoder
autoencoding
barcode
barcodes
bioconductor
bioinformatics
bronchoalveolar
buildNetwork
calculateEntropy
calculateFrequency
calculateGeneUsage
calculateMotif
calculateProperty
camelCase
checkBlanks
checkContigs
circlize
clonalAbundance
clonalBias
clonalBin
clonalCluster
clonalCompare
clonalDiversity
clonalFrequency
clonalHomeostasis
clonalLength
clonalNetwork
clonalOccupy
clonalOverlap
clonalOverlay
clonalProportion
clonalQuant
clonalRarefaction
clonalScatter
clonalSizeDistribution
clonally
cloneCall
cloneSize
cloneType
clonesizeDistribution
clonotype
clonotype's
clonotypeBias
clonotypeSizeDistribution
clonotypes
clusterTCR
colData
coldata
coloured
combineBCR
combineContig
combineExpression
combineSeurat
combineTCR
combineTRUST
combinedContig
compareClonotype
compareClonotypes
complementarity
compositional
constructConDFAndparseTCR
contig
contigs
convolutional
cpp
createHTOContigList
crucianiProperties
csv
cubature
dandelionR
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densityEnrichment
dev
df
dgCMatrix
distanc
doubletons
downsample
downsampled
downsampling
dplyr
dysregulation
edgeR
edgeR’s
embeddings
epitope
epitopes
erroring
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expa
explainability
exportClones
exportGraph
exportTable
fgsea
filterNonproductive
filteringMulti
formatGenes
frac
gapped
gd
geneRatio
generateSequences
geometricEncoder
germline
getCirclize
getCoord
getIMGT
geyserEnrichment
ggalluvial
ggdendrogram
ggfittext
ggplot
gini
github
gp
grabMeta
grey
greyed
groupBy
gseaEnrichment
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hammingCompare
heatmapEnrichment
hexbin
highlightClones
highlightClonotypes
humoral
hydrophobicity
hypermutation
hypervariable
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iNKT
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igraph
imgt
imm
immApex
immunarch
incongruent
inferCDR
inframe
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interpretability
inv
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jaccard
jk
json
kideraFactors
kmer
kmers
lapply
latform
leadingEdge
lengthContigs
lengthDF
levenshtein
ln
loadContigs
logFC
lvCompare
lvcompare
mB
mRNA
maTrex
makeGenes
markov
matric
maxlen
mer
migr
milo
miloR
morisita
msigdbr
mucosal
multiplets
multisystem
mutateSequences
na
nalysis
neighbourhood
neighbours
normalised
nrichment
nt
nucleotides
nw
occupiedClonotype
occupiedRepertoire
occupiedscRepertoire
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padj
palantir
parseAIRR
parseBCR
parseTCR
pca
penalises
percentAA
percentGeneUsage
percentGenes
percentKmer
percentVJ
performNormalization
physicochemical
pielou
pkgdown
positionalEntropy
positionalProperty
powerTCR
pre
probabilityMatrix
propertyEncoder
pseudobulk
pseudobulked
pseudobulks
pseudogenes
pseudotime
pval
quantContig
rda
readRDS
reclustering
regressClonotype
relevel
ridgeEnrichment
runEscape
runIbex
runPCA
runTrex
sampleType
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scater
scater's
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scatterClonotypes
scatterEnrichment
scoper
scran
screp
sequenceDecoder
sequenceEncoder
seurat
shannon
shazam
shm
simpson
splenocytes
splitEnrichment
ssGSEA
stScales
startrac
startstop
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subclones
subgraphs
subsetClones
subtype
subtypes
sw
tSNE
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tcrpheno
testthat
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tokenizeSequences
tokenizing
trackable
tran
transcriptional
transcriptomic
trex
truncdist
tsv
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unmutated
unreturned
variational
visVgene
visualise
vizCirclize
vizGene
vizGenes
vizVgene
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α
β
π
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