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.

Files in this package

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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