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tcR (version 2.0)

Advanced Data Analysis of T Cell Receptor Repertoires

Description

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

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Version

Install

install.packages('tcR')

Monthly Downloads

2

Version

2.0

License

Apache License 2.0

Maintainer

Vadim Nazarov

Last Published

May 14th, 2015

Functions in tcR (2.0)

AA_TABLE

Tables with genetic code.
codon.variants

Functions for working with aminoacid sequences.
sample2D

Get a sample from matrix with probabilities.
geneUsage

Gene usage.
matrixdiagcopy

Copy the up-triangle matrix values to low-triangle.
column.summary

Columns statistics.
group.clonotypes

Get all unique clonotypes.
vis.kmer.histogram

Plot of the most frequent kmers.
rarefaction

Diversity evaluation using rarefaction.
repOverlap

General function for the repertoire overlap evaluation.
pca.segments

Perform PCA on segments frequency data.
vis.number.count

Plot a histogram of counts.
parse.folder

Parse input table files with immune receptor repertoire data.
spectratyping

Spectratype plot.
barcodes.to.reads

Rearrange columns with counts for clonesets.
get.inframes

In-frame / out-of-frame sequences filter.
bootstrap.tcr

Bootstrap for data frames in package tcR.
generate.kmers

Generate k-mers.
vis.heatmap

Heatmap.
segments.alphabets

Alphabets of TCR and Ig gene segments.
startmitcr

Start MiTCR directly from the package.
permutedf

Shuffling data frames.
set.pb

Simple functions for manipulating progress bars.
get.deletions.alpha

Compute the number of deletions in MiTCR data frames.
segments.list

Segment data.
vis.count.len

Plot a histogram of lengths.
clonal.space.homeostasis

Clonal space homeostasis.
set.group.vector

Set group attribute for vertices of a mutation network
apply.symm

Apply function to every pair of data frames from a list.
find.clonotypes

Find target clonotypes and get columns' value corresponded to that clonotypes.
kmer.table

Make and manage the table of the most frequent k-mers.
beta.prob

List with assembling probabilities of beta chain TCRs.
check.distribution

Check for adequaty of distrubution.
get.n.barcodes

Resample data frame using values from the column with number of clonesets.
parse.cloneset

Parse input table files with the immune receptor repertoire data.
repDiversity

General function for the repertoire diversity estimation.
vis.top.proportions

Visualisation of top clones proportions.
revcomp

DNA reverse complementing and translation.
cosine.similarity

Set and vector similarity measures.
set.people.vector

Set and get attributes of a mutation network related to source people.
set.rank

Set new columns "Rank" and "Index".
cosine.sharing

Shared repertoire analysis.
contamination.stats

Contamination filtering.
get.kmers

Get kmers from sequences.
vis.clonal.dynamics

Visualise clonal dynamics among time points.
top.cross

Perform sequential cross starting from the top of a data frame.
vis.gene.usage

Histogram of segments usage.
vis.pca

PCA result visualisation
assymetry

Normalised log assymetry.
find.similar.sequences

Find similar sequences.
generate.tcr

Generate random nucleotide TCR sequences.
entropy

Information measures.
shared.repertoire

Shared TCR repertoire managing and analysis
inverse.simpson

Distribution evaluation.
vis.rarefaction

Rarefaction statistics visualisation.
vis.radarlike

Radar-like / spider-like plots.
gibbs.sampler

Gibbs Sampler.
loglikelihood

Log-likelihood.
mutation.network

Make mutation network for the given repertoire.
mutated.neighbours

Get vertex neighbours.
reverse.string

Reverse given character vector by the given n-plets.
cloneset.stats

MiTCR data frame basic statistics.
top.fun

Get samples from a repertoire slice-by-slice or top-by-top and apply function to them.
intersectClonesets

Intersection between sets of sequences or any elements.
get.all.substrings

Get all substrings for the given sequence.
tailbound.proportion

Proportions of specifyed subsets of clones.
twinsdata

Twins alpha-beta chain data
vis.clonal.space

Visualise occupied by clones homeostatic space among Samples or groups.
vis.logo

Logo - plots for amino acid and nucletide profiles.
gc.content

GC-content of a nucleotide sequences.
sample.clones

Get a random subset from a data.frame.
vis.group.boxplot

Boxplot for groups of observations.
entropy.seg

Repertoires' analysis using information measures applied to V- and J- segment frequencies.
has.class

Check if a given object has a given class.
kmer.profile

Profile of sequences of equal length.
convergence.index

Compute convergence characteristics of repertoires.