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tcR (version 1.1)
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
1.1
License
Apache License 2.0
Maintainer
Vadim Nazarov
Last Published
January 10th, 2015
Functions in tcR (1.1)
Search functions
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.