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tcR (version 2.1.1)

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

2.1.1

License

Apache License 2.0

Maintainer

Vadim Nazarov

Last Published

July 29th, 2015

Functions in tcR (2.1.1)

apply.symm

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

cosine.sharing

Shared repertoire analysis.

codon.variants

Functions for working with aminoacid sequences.

get.all.substrings

Get all substrings for the given sequence.

kmer.table

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

loglikelihood

Log-likelihood.

top.cross

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

segments.list

Segment data.

mutated.neighbours

Get vertex neighbours.

cloneset.stats

MiTCR data frame basic statistics.

find.similar.sequences

Find similar sequences.

shared.repertoire

Shared TCR repertoire managing and analysis

bootstrap.tcr

Bootstrap for data frames in package tcR.

rarefaction

Diversity evaluation using rarefaction.

sample.clones

Get a random subset from a data.frame.

vis.count.len

Plot a histogram of lengths.

entropy

Information measures.

convergence.index

Compute convergence characteristics of repertoires.

vis.top.proportions

Visualisation of top clones proportions.

AA_TABLE

Tables with genetic code.

geneUsage

Gene usage.

set.people.vector

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

gc.content

GC-content of a nucleotide sequences.

cosine.similarity

Set and vector similarity measures.

beta.prob

List with assembling probabilities of beta chain TCRs.

column.summary

Columns statistics.

mutation.network

Make mutation network for the given repertoire.

vis.number.count

Plot a histogram of counts.

entropy.seg

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

generate.tcr

Generate random nucleotide TCR sequences.

barcodes.to.reads

Rearrange columns with counts for clonesets.

get.n.barcodes

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

repOverlap

General function for the repertoire overlap evaluation.

parse.cloneset

Parse input table files with the immune receptor repertoire data.

group.clonotypes

Get all unique clonotypes.

revcomp

DNA reverse complementing and translation.

inverse.simpson

Distribution evaluation.

get.deletions.alpha

Compute the number of deletions in MiTCR data frames.

clonal.space.homeostasis

Clonal space homeostasis.

pca.segments

Perform PCA on segments frequency data.

permutedf

Shuffling data frames.

kmer.profile

Profile of sequences of equal length.

gibbs.sampler

Gibbs Sampler.

twinsdata

Twins alpha-beta chain data

top.fun

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

vis.logo

Logo - plots for amino acid and nucletide profiles.

vis.kmer.histogram

Plot of the most frequent kmers.

generate.kmers

Generate k-mers.

has.class

Check if a given object has a given class.

vis.clonal.space

Visualise occupied by clones homeostatic space among Samples or groups.

sample2D

Get a sample from matrix with probabilities.

get.inframes

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

parse.folder

Parse input table files with immune receptor repertoire data.

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

vis.clonal.dynamics

Visualise clonal dynamics among time points.

startmitcr

Start MiTCR directly from the package.

set.pb

Simple functions for manipulating progress bars.

vis.radarlike

Radar-like / spider-like plots.

vis.gene.usage

Histogram of segments usage.

tailbound.proportion

Proportions of specifyed subsets of clones.

repDiversity

General function for the repertoire diversity estimation.

intersectClonesets

Intersection between sets of sequences or any elements.

set.rank

Set new columns "Rank" and "Index".

vis.pca

PCA result visualisation

get.kmers

Get kmers from sequences.

contamination.stats

Contamination filtering.

matrixdiagcopy

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

fix.alleles

Fix alleles - remove allele informatio from columns with genes.

segments.alphabets

Alphabets of TCR and Ig gene segments.

assymetry

Normalised log assymetry.

check.distribution

Check for adequaty of distrubution.

reverse.string

Reverse given character vector by the given n-plets.

set.group.vector

Set group attribute for vertices of a mutation network

vis.group.boxplot

Boxplot for groups of observations.

vis.rarefaction

Rarefaction statistics visualisation.