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tcR (version 2.2.1.7)
Advanced Data Analysis of Immune Receptor Repertoires
Description
Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.
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Install
install.packages('tcR')
Monthly Downloads
140
Version
2.2.1.7
License
Apache License 2.0
Maintainer
Vadim Nazarov
Last Published
December 22nd, 2015
Functions in tcR (2.2.1.7)
Search functions
mutated.neighbours
Get vertex neighbours.
ozScore
Overlap Z-score.
column.summary
Columns statistics.
bootstrap.tcr
Bootstrap for data frames in package tcR.
contamination.stats
Contamination filtering.
group.clonotypes
Get all unique clonotypes.
codon.variants
Functions for working with aminoacid sequences.
loglikelihood
Log-likelihood.
find.clonotypes
Find target clonotypes and get columns' value corresponded to that clonotypes.
get.all.substrings
Get all substrings for the given sequence.
find.similar.sequences
Find similar sequences.
generate.kmers
Generate k-mers.
AA_TABLE
Tables with genetic code.
matrixSubgroups
Get all values from the matrix corresponding to specific groups.
fix.alleles
Fix alleles / genes by removing allele information / unnecessary colons.
cloneset.stats
MiTCR data frame basic statistics.
check.distribution
Check for adequaty of distrubution.
get.deletions.alpha
Compute the number of deletions in MiTCR data frames.
get.inframes
In-frame / out-of-frame sequences filter.
get.kmers
Get kmers from sequences.
pca.segments
Perform PCA on segments frequency data.
pca2euclid
Compute the Euclidean distance among principal components.
gc.content
GC-content of a nucleotide sequences.
repLoad
Parse input files or folders with immune receptor repertoire data.
barcodes.to.reads
Rearrange columns with counts for clonesets.
entropy
Information measures.
resample
Resample data frame using values from the column with number of clonesets.
cosine.similarity
Set and vector similarity measures.
clonal.space.homeostasis
Clonal space homeostasis.
vis.kmer.histogram
Plot of the most frequent kmers.
parse.folder
Parse input table files with immune receptor repertoire data.
set.group.vector
Set group attribute for vertices of a mutation network
vis.clonal.space
Visualise occupied by clones homeostatic space among Samples or groups.
permutedf
Shuffling data frames.
generate.tcr
Generate random nucleotide TCR sequences.
gibbs.sampler
Gibbs Sampler.
revcomp
DNA reverse complementing and translation.
repOverlap
General function for the repertoire overlap evaluation.
convergence.index
Compute convergence characteristics of repertoires.
kmer.profile
Profile of sequences of equal length.
kmer.table
Make and manage the table of the most frequent k-mers.
matrixdiagcopy
Copy the up-triangle matrix values to low-triangle.
vis.clonal.dynamics
Visualise clonal dynamics among time points.
apply.symm
Apply function to every pair of data frames from a list.
entropy.seg
Repertoires' analysis using information measures applied to V- and J- segment frequencies.
intersectClonesets
Intersection between sets of sequences or any elements.
has.class
Check if a given object has a given class.
geneUsage
Gene usage.
set.rank
Set new columns "Rank" and "Index".
set.people.vector
Set and get attributes of a mutation network related to source people.
repDiversity
General function for the repertoire diversity estimation.
vis.rarefaction
Rarefaction statistics visualisation.
vis.count.len
Plot a histogram of lengths.
inverse.simpson
Distribution evaluation.
segments.alphabets
Alphabets of TCR and Ig gene segments.
vis.shared.clonotypes
Visualisation of shared clonotypes occurrences among repertoires.
repSave
Save tcR data frames to disk as text files or gzipped text files.
vis.number.count
Plot a histogram of counts.
assymetry
Normalised log assymetry.
beta.prob
List with assembling probabilities of beta chain TCRs.
vis.heatmap
Heatmap.
shared.repertoire
Shared TCR repertoire managing and analysis
reverse.string
Reverse given character vector by the given n-plets.
rarefaction
Diversity evaluation using rarefaction.
vis.group.boxplot
Boxplot for groups of observations.
sample.clones
Get a random subset from a data.frame.
cosine.sharing
Shared repertoire analysis.
spectratyping
Spectratype plot.
permutDistTest
Monte Carlo permutation test for pairwise and one-vs-all-wise within- and inter-group differences in a set of repertoires.
vis.logo
Logo - plots for amino acid and nucletide profiles.
segments.list
Segment data.
tailbound.proportion
Proportions of specifyed subsets of clones.
vis.top.proportions
Visualisation of top clones proportions.
twinsdata
Twins alpha-beta chain data
top.cross
Perform sequential cross starting from the top of a data frame.
top.fun
Get samples from a repertoire slice-by-slice or top-by-top and apply function to them.
startmitcr
Start MiTCR directly from the package.
parse.cloneset
Parse input table files with the immune receptor repertoire data.
mutation.network
Make mutation network for the given repertoire.
sample2D
Get a sample from matrix with probabilities.
vis.radarlike
Radar-like / spider-like plots.
set.pb
Simple functions for manipulating progress bars.
vis.pca
PCA result visualisation
vis.gene.usage
Histogram of segments usage.