tcR: Advanced Data Analysis of Immune Receptor Repertoires

Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.

AuthorVadim Nazarov
Date of publication2016-04-22 13:10:15
MaintainerVadim Nazarov <vdm.nazarov@gmail.com>
LicenseApache License 2.0
Version2.2.1.11
http://imminfo.github.io/tcr/

View on CRAN

Man pages

AA_TABLE: Tables with genetic code.

apply.symm: Apply function to every pair of data frames from a list.

assymetry: Normalised log assymetry.

barcodes.to.reads: Rearrange columns with counts for clonesets.

beta.prob: List with assembling probabilities of beta chain TCRs.

bootstrap.tcr: Bootstrap for data frames in package tcR.

check.distribution: Check for adequaty of distrubution.

clonal.space.homeostasis: Clonal space homeostasis.

cloneset.stats: MiTCR data frame basic statistics.

codon.variants: Functions for working with aminoacid sequences.

column.summary: Columns statistics.

contamination.stats: Contamination filtering.

convergence.index: Compute convergence characteristics of repertoires.

cosine.sharing: Shared repertoire analysis.

cosine.similarity: Set and vector similarity measures.

entropy: Information measures.

entropy.seg: Repertoires' analysis using information measures applied to...

find.clonotypes: Find target clonotypes and get columns' value corresponded to...

find.similar.sequences: Find similar sequences.

fix.alleles: Fix alleles / genes by removing allele information /...

gc.content: GC-content of a nucleotide sequences.

generate.kmers: Generate k-mers.

generate.tcr: Generate random nucleotide TCR sequences.

geneUsage: Gene usage.

get.all.substrings: Get all substrings for the given sequence.

get.deletions.alpha: Compute the number of deletions in MiTCR data frames.

get.inframes: In-frame / out-of-frame sequences filter.

get.kmers: Get kmers from sequences.

gibbs.sampler: Gibbs Sampler.

group.clonotypes: Get all unique clonotypes.

has.class: Check if a given object has a given class.

intersectClonesets: Intersection between sets of sequences or any elements.

inverse.simpson: Distribution evaluation.

kmer.profile: Profile of sequences of equal length.

kmer.table: Make and manage the table of the most frequent k-mers.

loglikelihood: Log-likelihood.

matrixdiagcopy: Copy the up-triangle matrix values to low-triangle.

matrixSubgroups: Get all values from the matrix corresponding to specific...

mutated.neighbours: Get vertex neighbours.

mutation.network: Make mutation network for the given repertoire.

ozScore: Overlap Z-score.

parse.cloneset: Parse input table files with the immune receptor repertoire...

parse.folder: Parse input table files with immune receptor repertoire data.

pca2euclid: Compute the Euclidean distance among principal components.

pca.segments: Perform PCA on segments frequency data.

permutDistTest: Monte Carlo permutation test for pairwise and one-vs-all-wise...

permutedf: Shuffling data frames.

rarefaction: Diversity evaluation using rarefaction.

repDiversity: General function for the repertoire diversity estimation.

repLoad: Parse input files or folders with immune receptor repertoire...

repOverlap: General function for the repertoire overlap evaluation.

repSave: Save tcR data frames to disk as text files or gzipped text...

resample: Resample data frame using values from the column with number...

revcomp: DNA reverse complementing and translation.

reverse.string: Reverse given character vector by the given n-plets.

sample2D: Get a sample from matrix with probabilities.

sample.clones: Get a random subset from a data.frame.

segments.alphabets: Alphabets of TCR and Ig gene segments.

segments.list: Segment data.

set.group.vector: Set group attribute for vertices of a mutation network

set.pb: Simple functions for manipulating progress bars.

set.people.vector: Set and get attributes of a mutation network related to...

set.rank: Set new columns "Rank" and "Index".

shared.repertoire: Shared TCR repertoire managing and analysis

spectratyping: Spectratype plot.

startmitcr: Start MiTCR directly from the package.

tailbound.proportion: Proportions of specifyed subsets of clones.

top.cross: Perform sequential cross starting from the top of a data...

top.fun: Get samples from a repertoire slice-by-slice or top-by-top...

twinsdata: Twins alpha-beta chain data

vis.clonal.dynamics: Visualise clonal dynamics among time points.

vis.clonal.space: Visualise occupied by clones homeostatic space among Samples...

vis.count.len: Plot a histogram of lengths.

vis.gene.usage: Histogram of segments usage.

vis.group.boxplot: Boxplot for groups of observations.

vis.heatmap: Heatmap.

vis.kmer.histogram: Plot of the most frequent kmers.

vis.logo: Logo - plots for amino acid and nucletide profiles.

vis.number.count: Plot a histogram of counts.

vis.pca: PCA result visualisation

vis.radarlike: Radar-like / spider-like plots.

vis.rarefaction: Rarefaction statistics visualisation.

vis.shared.clonotypes: Visualisation of shared clonotypes occurrences among...

vis.top.proportions: Visualisation of top clones proportions.

Functions

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

Files

tcR
tcR/inst
tcR/inst/library.report.Rmd
tcR/inst/CITATION
tcR/inst/crossanalysis.report.Rmd
tcR/inst/doc
tcR/inst/doc/tcrvignette.Rmd
tcR/inst/doc/tcrvignette.R
tcR/inst/doc/tcrvignette.html
tcR/src
tcR/src/Makevars
tcR/src/neighbour.search.cpp
tcR/src/RcppExports.cpp
tcR/NAMESPACE
tcR/NEWS
tcR/data
tcR/data/twa.rda
tcR/data/beta.prob.rda
tcR/data/twb.rda
tcR/data/datalist
tcR/data/genesegments.rda
tcR/R
tcR/R/crosses.R tcR/R/infoanalysis.R tcR/R/spectrum.R tcR/R/dataproc.R tcR/R/filters.R tcR/R/mitcr.R tcR/R/repoverlap.R tcR/R/docdata.R tcR/R/shared.R tcR/R/kmers.R tcR/R/strtools.R tcR/R/plots.R tcR/R/io.R tcR/R/graph.R tcR/R/datatools.R tcR/R/RcppExports.R tcR/R/parsing.R tcR/R/repdiversity.R tcR/R/stats.R tcR/R/diversity.R tcR/R/segments.R tcR/R/measures.R
tcR/vignettes
tcR/vignettes/tcrvignette.Rmd
tcR/README.md
tcR/MD5
tcR/build
tcR/build/vignette.rds
tcR/DESCRIPTION
tcR/man
tcR/man/geneUsage.Rd tcR/man/entropy.seg.Rd tcR/man/vis.gene.usage.Rd tcR/man/mutated.neighbours.Rd tcR/man/parse.folder.Rd tcR/man/top.cross.Rd tcR/man/get.all.substrings.Rd tcR/man/set.rank.Rd tcR/man/entropy.Rd tcR/man/cosine.sharing.Rd tcR/man/assymetry.Rd tcR/man/intersectClonesets.Rd tcR/man/segments.list.Rd tcR/man/pca.segments.Rd tcR/man/rarefaction.Rd tcR/man/convergence.index.Rd tcR/man/group.clonotypes.Rd tcR/man/get.kmers.Rd tcR/man/bootstrap.tcr.Rd tcR/man/set.group.vector.Rd tcR/man/get.inframes.Rd tcR/man/AA_TABLE.Rd tcR/man/twinsdata.Rd tcR/man/vis.rarefaction.Rd tcR/man/vis.clonal.dynamics.Rd tcR/man/parse.cloneset.Rd tcR/man/loglikelihood.Rd tcR/man/gc.content.Rd tcR/man/set.people.vector.Rd tcR/man/tailbound.proportion.Rd tcR/man/vis.number.count.Rd tcR/man/kmer.profile.Rd tcR/man/permutedf.Rd tcR/man/revcomp.Rd tcR/man/vis.logo.Rd tcR/man/set.pb.Rd tcR/man/top.fun.Rd tcR/man/repSave.Rd tcR/man/spectratyping.Rd tcR/man/barcodes.to.reads.Rd tcR/man/vis.count.len.Rd tcR/man/vis.radarlike.Rd tcR/man/cloneset.stats.Rd tcR/man/segments.alphabets.Rd tcR/man/apply.symm.Rd tcR/man/gibbs.sampler.Rd tcR/man/startmitcr.Rd tcR/man/matrixdiagcopy.Rd tcR/man/resample.Rd tcR/man/beta.prob.Rd tcR/man/codon.variants.Rd tcR/man/vis.pca.Rd tcR/man/find.clonotypes.Rd tcR/man/vis.top.proportions.Rd tcR/man/get.deletions.alpha.Rd tcR/man/vis.heatmap.Rd tcR/man/has.class.Rd tcR/man/ozScore.Rd tcR/man/clonal.space.homeostasis.Rd tcR/man/mutation.network.Rd tcR/man/vis.group.boxplot.Rd tcR/man/generate.kmers.Rd tcR/man/inverse.simpson.Rd tcR/man/cosine.similarity.Rd tcR/man/kmer.table.Rd tcR/man/reverse.string.Rd tcR/man/vis.kmer.histogram.Rd tcR/man/sample.clones.Rd tcR/man/fix.alleles.Rd tcR/man/sample2D.Rd tcR/man/repDiversity.Rd tcR/man/find.similar.sequences.Rd tcR/man/column.summary.Rd tcR/man/repOverlap.Rd tcR/man/generate.tcr.Rd tcR/man/pca2euclid.Rd tcR/man/contamination.stats.Rd tcR/man/check.distribution.Rd tcR/man/permutDistTest.Rd tcR/man/vis.shared.clonotypes.Rd tcR/man/matrixSubgroups.Rd tcR/man/vis.clonal.space.Rd tcR/man/repLoad.Rd tcR/man/shared.repertoire.Rd

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