Advanced Data Analysis of Immune Receptor Repertoires

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 |

spectratype | Spectratype |

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. |

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