tcR: Advanced Data Analysis of Immune Receptor Repertoires

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Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.

Author
Vadim Nazarov
Date of publication
2016-04-22 13:10:15
Maintainer
Vadim Nazarov <vdm.nazarov@gmail.com>
License
Apache License 2.0
Version
2.2.1.11
URLs

View on CRAN

Man pages

AA_TABLE
Tables with genetic code.
apply.symm
Apply function to every pair of data frames from a list.
assymetry
Normalised log assymetry.
barcodes.to.reads
Rearrange columns with counts for clonesets.
beta.prob
List with assembling probabilities of beta chain TCRs.
bootstrap.tcr
Bootstrap for data frames in package tcR.
check.distribution
Check for adequaty of distrubution.
clonal.space.homeostasis
Clonal space homeostasis.
cloneset.stats
MiTCR data frame basic statistics.
codon.variants
Functions for working with aminoacid sequences.
column.summary
Columns statistics.
contamination.stats
Contamination filtering.
convergence.index
Compute convergence characteristics of repertoires.
cosine.sharing
Shared repertoire analysis.
cosine.similarity
Set and vector similarity measures.
entropy
Information measures.
entropy.seg
Repertoires' analysis using information measures applied to...
find.clonotypes
Find target clonotypes and get columns' value corresponded to...
find.similar.sequences
Find similar sequences.
fix.alleles
Fix alleles / genes by removing allele information /...
gc.content
GC-content of a nucleotide sequences.
generate.kmers
Generate k-mers.
generate.tcr
Generate random nucleotide TCR sequences.
geneUsage
Gene usage.
get.all.substrings
Get all substrings for the given sequence.
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.
gibbs.sampler
Gibbs Sampler.
group.clonotypes
Get all unique clonotypes.
has.class
Check if a given object has a given class.
intersectClonesets
Intersection between sets of sequences or any elements.
inverse.simpson
Distribution evaluation.
kmer.profile
Profile of sequences of equal length.
kmer.table
Make and manage the table of the most frequent k-mers.
loglikelihood
Log-likelihood.
matrixdiagcopy
Copy the up-triangle matrix values to low-triangle.
matrixSubgroups
Get all values from the matrix corresponding to specific...
mutated.neighbours
Get vertex neighbours.
mutation.network
Make mutation network for the given repertoire.
ozScore
Overlap Z-score.
parse.cloneset
Parse input table files with the immune receptor repertoire...
parse.folder
Parse input table files with immune receptor repertoire data.
pca2euclid
Compute the Euclidean distance among principal components.
pca.segments
Perform PCA on segments frequency data.
permutDistTest
Monte Carlo permutation test for pairwise and one-vs-all-wise...
permutedf
Shuffling data frames.
rarefaction
Diversity evaluation using rarefaction.
repDiversity
General function for the repertoire diversity estimation.
repLoad
Parse input files or folders with immune receptor repertoire...
repOverlap
General function for the repertoire overlap evaluation.
repSave
Save tcR data frames to disk as text files or gzipped text...
resample
Resample data frame using values from the column with number...
revcomp
DNA reverse complementing and translation.
reverse.string
Reverse given character vector by the given n-plets.
sample2D
Get a sample from matrix with probabilities.
sample.clones
Get a random subset from a data.frame.
segments.alphabets
Alphabets of TCR and Ig gene segments.
segments.list
Segment data.
set.group.vector
Set group attribute for vertices of a mutation network
set.pb
Simple functions for manipulating progress bars.
set.people.vector
Set and get attributes of a mutation network related to...
set.rank
Set new columns "Rank" and "Index".
shared.repertoire
Shared TCR repertoire managing and analysis
spectratyping
Spectratype plot.
startmitcr
Start MiTCR directly from the package.
tailbound.proportion
Proportions of specifyed subsets of clones.
top.cross
Perform sequential cross starting from the top of a data...
top.fun
Get samples from a repertoire slice-by-slice or top-by-top...
twinsdata
Twins alpha-beta chain data
vis.clonal.dynamics
Visualise clonal dynamics among time points.
vis.clonal.space
Visualise occupied by clones homeostatic space among Samples...
vis.count.len
Plot a histogram of lengths.
vis.gene.usage
Histogram of segments usage.
vis.group.boxplot
Boxplot for groups of observations.
vis.heatmap
Heatmap.
vis.kmer.histogram
Plot of the most frequent kmers.
vis.logo
Logo - plots for amino acid and nucletide profiles.
vis.number.count
Plot a histogram of counts.
vis.pca
PCA result visualisation
vis.radarlike
Radar-like / spider-like plots.
vis.rarefaction
Rarefaction statistics visualisation.
vis.shared.clonotypes
Visualisation of shared clonotypes occurrences among...
vis.top.proportions
Visualisation of top clones proportions.

Files in this package

tcR
tcR/inst
tcR/inst/library.report.Rmd
tcR/inst/CITATION
tcR/inst/crossanalysis.report.Rmd
tcR/inst/doc
tcR/inst/doc/tcrvignette.Rmd
tcR/inst/doc/tcrvignette.R
tcR/inst/doc/tcrvignette.html
tcR/src
tcR/src/Makevars
tcR/src/neighbour.search.cpp
tcR/src/RcppExports.cpp
tcR/NAMESPACE
tcR/NEWS
tcR/data
tcR/data/twa.rda
tcR/data/beta.prob.rda
tcR/data/twb.rda
tcR/data/datalist
tcR/data/genesegments.rda
tcR/R
tcR/R/crosses.R
tcR/R/infoanalysis.R
tcR/R/spectrum.R
tcR/R/dataproc.R
tcR/R/filters.R
tcR/R/mitcr.R
tcR/R/repoverlap.R
tcR/R/docdata.R
tcR/R/shared.R
tcR/R/kmers.R
tcR/R/strtools.R
tcR/R/plots.R
tcR/R/io.R
tcR/R/graph.R
tcR/R/datatools.R
tcR/R/RcppExports.R
tcR/R/parsing.R
tcR/R/repdiversity.R
tcR/R/stats.R
tcR/R/diversity.R
tcR/R/segments.R
tcR/R/measures.R
tcR/vignettes
tcR/vignettes/tcrvignette.Rmd
tcR/README.md
tcR/MD5
tcR/build
tcR/build/vignette.rds
tcR/DESCRIPTION
tcR/man
tcR/man/geneUsage.Rd
tcR/man/entropy.seg.Rd
tcR/man/vis.gene.usage.Rd
tcR/man/mutated.neighbours.Rd
tcR/man/parse.folder.Rd
tcR/man/top.cross.Rd
tcR/man/get.all.substrings.Rd
tcR/man/set.rank.Rd
tcR/man/entropy.Rd
tcR/man/cosine.sharing.Rd
tcR/man/assymetry.Rd
tcR/man/intersectClonesets.Rd
tcR/man/segments.list.Rd
tcR/man/pca.segments.Rd
tcR/man/rarefaction.Rd
tcR/man/convergence.index.Rd
tcR/man/group.clonotypes.Rd
tcR/man/get.kmers.Rd
tcR/man/bootstrap.tcr.Rd
tcR/man/set.group.vector.Rd
tcR/man/get.inframes.Rd
tcR/man/AA_TABLE.Rd
tcR/man/twinsdata.Rd
tcR/man/vis.rarefaction.Rd
tcR/man/vis.clonal.dynamics.Rd
tcR/man/parse.cloneset.Rd
tcR/man/loglikelihood.Rd
tcR/man/gc.content.Rd
tcR/man/set.people.vector.Rd
tcR/man/tailbound.proportion.Rd
tcR/man/vis.number.count.Rd
tcR/man/kmer.profile.Rd
tcR/man/permutedf.Rd
tcR/man/revcomp.Rd
tcR/man/vis.logo.Rd
tcR/man/set.pb.Rd
tcR/man/top.fun.Rd
tcR/man/repSave.Rd
tcR/man/spectratyping.Rd
tcR/man/barcodes.to.reads.Rd
tcR/man/vis.count.len.Rd
tcR/man/vis.radarlike.Rd
tcR/man/cloneset.stats.Rd
tcR/man/segments.alphabets.Rd
tcR/man/apply.symm.Rd
tcR/man/gibbs.sampler.Rd
tcR/man/startmitcr.Rd
tcR/man/matrixdiagcopy.Rd
tcR/man/resample.Rd
tcR/man/beta.prob.Rd
tcR/man/codon.variants.Rd
tcR/man/vis.pca.Rd
tcR/man/find.clonotypes.Rd
tcR/man/vis.top.proportions.Rd
tcR/man/get.deletions.alpha.Rd
tcR/man/vis.heatmap.Rd
tcR/man/has.class.Rd
tcR/man/ozScore.Rd
tcR/man/clonal.space.homeostasis.Rd
tcR/man/mutation.network.Rd
tcR/man/vis.group.boxplot.Rd
tcR/man/generate.kmers.Rd
tcR/man/inverse.simpson.Rd
tcR/man/cosine.similarity.Rd
tcR/man/kmer.table.Rd
tcR/man/reverse.string.Rd
tcR/man/vis.kmer.histogram.Rd
tcR/man/sample.clones.Rd
tcR/man/fix.alleles.Rd
tcR/man/sample2D.Rd
tcR/man/repDiversity.Rd
tcR/man/find.similar.sequences.Rd
tcR/man/column.summary.Rd
tcR/man/repOverlap.Rd
tcR/man/generate.tcr.Rd
tcR/man/pca2euclid.Rd
tcR/man/contamination.stats.Rd
tcR/man/check.distribution.Rd
tcR/man/permutDistTest.Rd
tcR/man/vis.shared.clonotypes.Rd
tcR/man/matrixSubgroups.Rd
tcR/man/vis.clonal.space.Rd
tcR/man/repLoad.Rd
tcR/man/shared.repertoire.Rd