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tcR (version 1.3)

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')

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Version

1.3

License

Apache License 2.0

Maintainer

Vadim Nazarov

Last Published

March 21st, 2015

Functions in tcR (1.3)

contamination.stats

Contamination filtering.

AA_TABLE

Tables with genetic code.

vis.kmer.histogram

Plot of the most frequent kmers.

kmer.table

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

mitcr.stats

MiTCR data frame basic statistics.

segments.list

Segment data.

barcodes.to.reads

Rearrange columns with counts for clonesets.

intersect

Intersection between sets of sequences or any elements.

parse.folder

Parse input table files with immune receptor repertoire data.

convergence.index

Compute convergence characteristics of repertoires.

gc.content

GC-content of a nucleotide sequences.

segments.alphabets

Alphabets of TCR and Ig gene segments.

get.inframes

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

spectratyping

Spectratype plot.

check.distribution

Check for adequaty of distrubution.

bootstrap.tcr

Bootstrap for data frames in package tcR.

get.n.barcodes

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

gibbs.sampler

Gibbs Sampler.

assymetry

Normalised log assymetry.

cosine.sharing

Shared repertoire analysis.

generate.tcr

Generate random nucleotide TCR sequences.

startmitcr

Start MiTCR directly from the package.

mutated.neighbours

Get vertex neighbours.

matrixdiagcopy

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

tailbound.proportion

Proportions of specifyed subsets of clones.

generate.kmers

Generate k-mers.

vis.clonal.dynamics

Visualise clonal dynamics among time points.

vis.V.usage

Histogram of segments usage.

permutedf

Shuffling data frames.

shared.repertoire

Shared TCR repertoire managing and analysis

vis.radarlike

Radar-like / spider-like plots.

vis.pca

PCA result visualisation

get.deletions.alpha

Compute the number of deletions in MiTCR data frames.

vis.count.len

Plot a histogram of lengths.

loglikelihood

Log-likelihood.

top.cross

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

rarefaction

Diversity evaluation using rarefaction.

vis.clonal.space

Visualise occupied by clones homeostatic space among subjects or groups.

column.summary

Columns statistics.

vis.logo

Logo - plots for amino acid and nucletide profiles.

freq.segments

V- and J-segments frequency.

entropy.seg

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

set.rank

Set new columns "Rank" and "Index".

vis.number.count

Plot a histogram of counts.

apply.symm

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

sample.clones

Get a random subset from a data.frame.

cosine.similarity

Set and vector similarity measures.

vis.top.proportions

Visualisation of top clones proportions.

mutation.network

Make mutation network for the given repertoire.

find.similar.sequences

Find similar sequences.

get.all.substrings

Get all substrings for the given sequence.

beta.prob

List with assembling probabilities of beta chain TCRs.

reverse.string

Reverse given character vector by the given n-plets.

inverse.simpson

Distribution evaluation.

vis.group.boxplot

Boxplot for groups of observations.

entropy

Information measures.

find.clonotypes

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

vis.heatmap

Heatmap.

sample2D

Get a sample from matrix with probabilities.

has.class

Check if a given object has a given class.

set.group.vector

Set group attribute for vertices of a mutation network

parse.cloneset

Parse input table files with immune receptor repertoire data.

vis.rarefaction

Rarefaction statistics visualisation.

clonal.space.homeostasis

Clonal space homeostasis.

set.people.vector

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

twinsdata

Twins alpha-beta chain data

codon.variants

Functions for working with aminoacid sequences.

pca.segments

Perform PCA on segments frequency data.

get.kmers

Get kmers from sequences.

top.fun

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

set.pb

Simple functions for manipulating progress bars.

revcomp

DNA reverse complementing and translation.

group.clonotypes

Get all unique clonotypes.

kmer.profile

Profile of sequences of equal length.