tcR: Advanced Data Analysis of Immune Receptor Repertoires
Version 2.2.1.11

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
URL http://imminfo.github.io/tcr/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("tcR")

Getting started

README.md
<center> <h1>tcR: a package for T cell receptor and Immunoglobulin repertoires advanced data analysis</h1>

Popular man pages

cloneset.stats: MiTCR data frame basic statistics.
cosine.sharing: Shared repertoire analysis.
cosine.similarity: Set and vector similarity measures.
geneUsage: Gene usage.
parse.folder: Parse input table files with immune receptor repertoire data.
shared.repertoire: Shared TCR repertoire managing and analysis
vis.radarlike: Radar-like / spider-like plots.
See all...

All man pages Function index File listing

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
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
MACMUL_TRBJ Man page
MACMUL_TRBV 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
add.legend Source code
add.pb Man page Source code
apply.asymm Man page Source code
apply.symm Man page Source code
assymetry Man page Source code
barcodes.to.reads Man page Source code
beta.prob Man page
blues.gradient Source code
bootstrap.tcr Man page Source code
bunch.translate Man page Source code
chao1 Man page Source code
check.distribution Man page Source code
clonal.proportion Man page Source code
clonal.space.homeostasis Man page Source code
cloneset.stats Man page Source code
clonotypescount Man page Source code
codon.variants Man page Source code
colourblind.discrete Source code
colourblind.discrete2 Source code
colourblind.gradient Source code
column.choice Source code
column.summary Man page Source code
contamination.stats Man page Source code
convergence.index Man page Source code
cosine.sharing Man page Source code
cosine.similarity Man page Source code
count.frames Man page Source code
count.inframes Man page Source code
count.outframes Man page Source code
decontamination Man page Source code
diversity Man page Source code
downsample Man page Source code
entropy Man page Source code
entropy.seg Man page Source code
exact.match Man page Source code
exact_search Source code
exact_search2 Source code
exact_search_list Source code
find.clonotypes Man page Source code
find.similar.sequences Man page Source code
fix.alleles Man page Source code
fix.genes Man page Source code
fix.listnames Source code
fix.segments Source code
gc.content Man page Source code
geneUsage Man page Source code
genealphabets Man page
generate.kmers Man page Source code
generate.kmers.prob Man page Source code
generate.tcr Man page Source code
genesegments Man page
get.all.substrings Man page Source code
get.deletions.alpha Man page Source code
get.deletions.beta Man page Source code
get.frames Man page Source code
get.group.names Man page Source code
get.inframes Man page Source code
get.kmer.column Man page Source code
get.kmers Man page Source code
get.outframes Man page Source code
get.people.names Man page Source code
gibbs.sampler Man page Source code
gini Man page Source code
gini.simpson Man page Source code
group.clonotypes Man page Source code
hamming.match Man page Source code
hamming_search Source code
has.class Man page Source code
horn.index Man page Source code
insertion.stats Man page Source code
intersectClonesets Man page Source code
intersectCount Man page Source code
intersectIndices Man page Source code
intersectLogic Man page Source code
inverse.simpson Man page Source code
jaccard.index Man page Source code
js.div Man page Source code
js.div.seg Man page Source code
kl.div Man page Source code
kmer.profile Man page Source code
kmer.table Man page Source code
kmers.profile Man page
levenshtein.match Man page Source code
levenshtein_search Source code
loglikelihood Man page Source code
matrixSubgroups Man page Source code
matrixdiagcopy Man page Source code
morisitas.index Man page Source code
mutated.neighbours Man page Source code
mutation.network Man page Source code
overlap.coef Man page Source code
ozScore Man page Source code
parse.cloneset Man page Source code
parse.file Man page Source code
parse.file.list Man page Source code
parse.folder Man page Source code
parse.immunoseq Man page Source code
parse.immunoseq2 Man page Source code
parse.immunoseq3 Man page Source code
parse.imseq Man page Source code
parse.migec Man page Source code
parse.migmap Man page Source code
parse.mitcr Man page Source code
parse.mitcrbc Man page Source code
parse.mixcr Man page Source code
parse.tcr Man page Source code
parse.vdjtools Man page Source code
pca.segments Man page Source code
pca.segments.2D Man page Source code
pca2euclid Man page Source code
permutDistTest Man page Source code
permutedf Man page Source code
rarefaction Man page Source code
repDiversity Man page Source code
repLoad Man page Source code
repOverlap Man page Source code
repSave Man page Source code
repseq.stats Man page Source code
resample Man page Source code
revcomp Man page Source code
reverse.string Man page Source code
reverse.translation Man page Source code
ryg.gradient Source code
sample.clones Man page Source code
sample2D Man page Source code
segments.alphabets Man page
segments.list Man page
set.attr Source code
set.group.vector Man page Source code
set.index Man page Source code
set.pb Man page Source code
set.people.vector Man page Source code
set.rank Man page Source code
shared.clones.count Man page Source code
shared.matrix Man page Source code
shared.repertoire Man page Source code
shared.representation Man page Source code
shared.summary Man page Source code
similarity Man page
slice.fun Man page Source code
spectratyping Man page Source code
split.get Source code
startmitcr Man page Source code
tailbound.proportion Man page Source code
top.cross Man page Source code
top.cross.plot Man page Source code
top.cross.vec Man page Source code
top.fun Man page Source code
top.proportion Man page Source code
translated.nucl.sequences Man page Source code
tversky.index Man page Source code
twa Man page
twb Man page
twinsdata Man page
unpermutedf Man page Source code
verbose.msg Source code
vis.J.usage Man page
vis.V.usage Man page
vis.clonal.dynamics Man page Source code
vis.clonal.space Man page Source code
vis.count.len Man page Source code
vis.gene.usage Man page Source code
vis.group.boxplot Man page Source code
vis.heatmap Man page Source code
vis.kmer.histogram Man page Source code
vis.logo Man page Source code
vis.number.count Man page Source code
vis.pca Man page Source code
vis.radarlike Man page Source code
vis.rarefaction Man page Source code
vis.shared.clonotypes Man page Source code
vis.top.proportions Man page Source code

Files

inst
inst/library.report.Rmd
inst/CITATION
inst/crossanalysis.report.Rmd
inst/doc
inst/doc/tcrvignette.Rmd
inst/doc/tcrvignette.R
inst/doc/tcrvignette.html
src
src/Makevars
src/neighbour.search.cpp
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/twa.rda
data/beta.prob.rda
data/twb.rda
data/datalist
data/genesegments.rda
R
R/crosses.R
R/infoanalysis.R
R/spectrum.R
R/dataproc.R
R/filters.R
R/mitcr.R
R/repoverlap.R
R/docdata.R
R/shared.R
R/kmers.R
R/strtools.R
R/plots.R
R/io.R
R/graph.R
R/datatools.R
R/RcppExports.R
R/parsing.R
R/repdiversity.R
R/stats.R
R/diversity.R
R/segments.R
R/measures.R
vignettes
vignettes/tcrvignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/geneUsage.Rd
man/entropy.seg.Rd
man/vis.gene.usage.Rd
man/mutated.neighbours.Rd
man/parse.folder.Rd
man/top.cross.Rd
man/get.all.substrings.Rd
man/set.rank.Rd
man/entropy.Rd
man/cosine.sharing.Rd
man/assymetry.Rd
man/intersectClonesets.Rd
man/segments.list.Rd
man/pca.segments.Rd
man/rarefaction.Rd
man/convergence.index.Rd
man/group.clonotypes.Rd
man/get.kmers.Rd
man/bootstrap.tcr.Rd
man/set.group.vector.Rd
man/get.inframes.Rd
man/AA_TABLE.Rd
man/twinsdata.Rd
man/vis.rarefaction.Rd
man/vis.clonal.dynamics.Rd
man/parse.cloneset.Rd
man/loglikelihood.Rd
man/gc.content.Rd
man/set.people.vector.Rd
man/tailbound.proportion.Rd
man/vis.number.count.Rd
man/kmer.profile.Rd
man/permutedf.Rd
man/revcomp.Rd
man/vis.logo.Rd
man/set.pb.Rd
man/top.fun.Rd
man/repSave.Rd
man/spectratyping.Rd
man/barcodes.to.reads.Rd
man/vis.count.len.Rd
man/vis.radarlike.Rd
man/cloneset.stats.Rd
man/segments.alphabets.Rd
man/apply.symm.Rd
man/gibbs.sampler.Rd
man/startmitcr.Rd
man/matrixdiagcopy.Rd
man/resample.Rd
man/beta.prob.Rd
man/codon.variants.Rd
man/vis.pca.Rd
man/find.clonotypes.Rd
man/vis.top.proportions.Rd
man/get.deletions.alpha.Rd
man/vis.heatmap.Rd
man/has.class.Rd
man/ozScore.Rd
man/clonal.space.homeostasis.Rd
man/mutation.network.Rd
man/vis.group.boxplot.Rd
man/generate.kmers.Rd
man/inverse.simpson.Rd
man/cosine.similarity.Rd
man/kmer.table.Rd
man/reverse.string.Rd
man/vis.kmer.histogram.Rd
man/sample.clones.Rd
man/fix.alleles.Rd
man/sample2D.Rd
man/repDiversity.Rd
man/find.similar.sequences.Rd
man/column.summary.Rd
man/repOverlap.Rd
man/generate.tcr.Rd
man/pca2euclid.Rd
man/contamination.stats.Rd
man/check.distribution.Rd
man/permutDistTest.Rd
man/vis.shared.clonotypes.Rd
man/matrixSubgroups.Rd
man/vis.clonal.space.Rd
man/repLoad.Rd
man/shared.repertoire.Rd
tcR documentation built on May 19, 2017, 9:48 p.m.

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