tcR v1.1

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by Vadim Nazarov

Data Analysis of T-cell Receptor Repertoires

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

Functions in tcR

Name Description
get.all.substrings Get all substrings for the given sequence.
entropy Information measures.
permutedf Shuffling data frames.
AA_TABLE Tables with genetic code.
reverse.string Reverse given character vector by the given n-plets.
get.deletions.alpha Compute the number of deletions in MiTCR data frames.
rarefaction Diversity evaluation using rarefaction.
generate.tcr Generate random nucleotide TCR sequences.
check.distribution Check for adequaty of distrubution.
startmitcr Start MiTCR directly from the package.
gc.content GC-content of a nucleotide sequences.
beta.prob List with assembling probabilities of beta chain TCRs.
set.rank Set new columns "Rank" and "Index".
contamination.stats Contamination filtering.
mitcr.stats MiTCR data frame basic statistics.
inverse.simpson Distribution evaluation.
revcomp DNA reverse complementing and translation.
parse.file.list Parse files from the given vector or list with filepaths and return list with data.frames.
intersect Intersection between sets of sequences or any elements.
top.cross Perform sequential cross starting from the top of a data.frame.
parse.file Parse input file with the given filename to a data frame.
get.inframes In-frame / out-of-frame sequences filter.
barcodes.to.reads Rearrange columns with counts for clonesets.
find.clonotypes Find target clonotypes and get columns' value corresponded to that clonotypes.
set.pb Simple functions for manipulating progress bars.
vis.heatmap Heatmap.
codon.variants Functions for working with aminoacid sequences.
entropy.seg Repertoires' analysis using information measures applied to V- and J- segment frequencies.
freq.segments V- and J-segments frequency.
apply.symm Apply function to every pair of data frames from a list.
convergence.index Compute convergence characteristics of repertoires.
bootstrap.tcr Bootstrap for data frames in package tcR.
generate.kmers Generate k-mers.
cosine.similarity Set and vector similarity measures.
vis.pca PCA result visualisation
vis.top.proportions Visualisation of top clones proportions.
column.summary Columns statistics.
loglikelihood Log-likelihood.
sample2D Get a sample from matrix with probabilities.
gibbs.sampler Gibbs Sampler.
get.n.barcodes Resample data frame using values from the column with number of clonesets.
shared.repertoire Shared TCR repertoire managing and analysis
top.fun Get samples from a repertoire slice-by-slice or top-by-top and apply function to them.
spectratyping Spectratype plot.
twinsdata Twins alpha-beta chain data
segments.list Segment data.
vis.V.usage Histogram of segments usage.
pca.segments Perform PCA on segments frequency data.
assymetry Normalised log assymetry.
segments.alphabets Alphabets of V-J segments.
vis.number.count Plot a histogram of counts.
sample.clones Get a random subset from a data.frame.
tailbound.proportion Proportions of specifyed subsets of clones.
find.similar.sequences Find similar sequences.
vis.kmer.histogram Plot of the most frequent kmers.
has.class Check if a given object has a given class.
vis.count.len Plot a histogram of lengths.
vis.rarefaction Rarefaction statistics visualisation.
vis.clonal.dynamics Visualise clonal dynamics among time points.
get.kmers Get kmers from sequences.
kmer.table Make and manage the table of the most frequent k-mers.
kmer.profile Profile of sequences of equal length.
parse.folder Parse all files to dataframes from the given path to folder.
matrixdiagcopy Copy the up-triangle matrix values to low-triangle.
cosine.sharing Shared repertoire analysis.
vis.radarlike Radar-like / spider-like plots.
vis.group.boxplot Boxplot for groups of observations.
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Details

Type Package
Date 2014-12-12
License Apache License 2.0
LinkingTo Rcpp
Packaged 2015-01-10 18:04:26 UTC; ripley
NeedsCompilation yes
Repository CRAN
Date/Publication 2015-01-10 19:06:05

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