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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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Install
install.packages('tcR')
Monthly Downloads
140
Version
2.1.1
License
Apache License 2.0
Maintainer
Vadim Nazarov
Last Published
July 29th, 2015
Functions in tcR (2.1.1)
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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.
spectratyping
Spectratype plot.
vis.heatmap
Heatmap.
find.clonotypes
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.