A B C D E F G H I J K L M O P R S T U V misc
| AA_TABLE | Tables with genetic code. |
| AA_TABLE_REVERSED | Tables with genetic code. |
| add.pb | Simple functions for manipulating progress bars. |
| apply.asymm | Apply function to every pair of data frames from a list. |
| 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. |
| bunch.translate | DNA reverse complementing and translation. |
| chao1 | Distribution evaluation. |
| check.distribution | Check for adequaty of distrubution. |
| clonal.proportion | Proportions of specifyed subsets of clones. |
| clonal.space.homeostasis | Clonal space homeostasis. |
| cloneset.stats | MiTCR data frame basic statistics. |
| clonotypescount | In-frame / out-of-frame sequences filter. |
| 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. |
| count.frames | In-frame / out-of-frame sequences filter. |
| count.inframes | In-frame / out-of-frame sequences filter. |
| count.outframes | In-frame / out-of-frame sequences filter. |
| decontamination | Contamination filtering. |
| diversity | Distribution evaluation. |
| downsample | Resample data frame using values from the column with number of clonesets. |
| entropy | Information measures. |
| entropy.seg | Repertoires' analysis using information measures applied to V- and J- segment frequencies. |
| exact.match | Find similar sequences. |
| find.clonotypes | Find target clonotypes and get columns' value corresponded to that clonotypes. |
| find.similar.sequences | Find similar sequences. |
| fix.alleles | Fix alleles / genes by removing allele information / unnecessary colons. |
| fix.genes | Fix alleles / genes by removing allele information / unnecessary colons. |
| gc.content | GC-content of a nucleotide sequences. |
| genealphabets | Alphabets of TCR and Ig gene segments. |
| generate.kmers | Generate k-mers. |
| generate.kmers.prob | Generate k-mers. |
| generate.tcr | Generate random nucleotide TCR sequences. |
| genesegments | Segment data. |
| 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.deletions.beta | Compute the number of deletions in MiTCR data frames. |
| get.frames | In-frame / out-of-frame sequences filter. |
| get.group.names | Set group attribute for vertices of a mutation network |
| get.inframes | In-frame / out-of-frame sequences filter. |
| get.kmer.column | Make and manage the table of the most frequent k-mers. |
| get.kmers | Get kmers from sequences. |
| get.outframes | In-frame / out-of-frame sequences filter. |
| get.people.names | Set and get attributes of a mutation network related to source people. |
| gibbs.sampler | Gibbs Sampler. |
| gini | Distribution evaluation. |
| gini.simpson | Distribution evaluation. |
| group.clonotypes | Get all unique clonotypes. |
| hamming.match | Find similar sequences. |
| has.class | Check if a given object has a given class. |
| horn.index | Set and vector similarity measures. |
| HUMAN_IGHD | Alphabets of TCR and Ig gene segments. |
| HUMAN_IGHJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_IGHV | Alphabets of TCR and Ig gene segments. |
| HUMAN_IGKJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_IGKV | Alphabets of TCR and Ig gene segments. |
| HUMAN_IGLJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_IGLV | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRAJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRAV | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBD | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBV | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBV_ALS | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBV_FAM | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBV_GEN | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRBV_MITCR | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRDD | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRDJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRDV | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRGJ | Alphabets of TCR and Ig gene segments. |
| HUMAN_TRGV | Alphabets of TCR and Ig gene segments. |
| insertion.stats | Columns statistics. |
| intersectClonesets | Intersection between sets of sequences or any elements. |
| intersectCount | Intersection between sets of sequences or any elements. |
| intersectIndices | Intersection between sets of sequences or any elements. |
| intersectLogic | Intersection between sets of sequences or any elements. |
| inverse.simpson | Distribution evaluation. |
| jaccard.index | Set and vector similarity measures. |
| js.div | Information measures. |
| js.div.seg | Repertoires' analysis using information measures applied to V- and J- segment frequencies. |
| kl.div | Information measures. |
| kmer.profile | Profile of sequences of equal length. |
| kmer.table | Make and manage the table of the most frequent k-mers. |
| kmers.profile | Profile of sequences of equal length. |
| levenshtein.match | Find similar sequences. |
| loglikelihood | Log-likelihood. |
| MACMUL_TRBJ | Alphabets of TCR and Ig gene segments. |
| MACMUL_TRBV | Alphabets of TCR and Ig gene segments. |
| matrixdiagcopy | Copy the up-triangle matrix values to low-triangle. |
| matrixSubgroups | Get all values from the matrix corresponding to specific groups. |
| morisitas.index | Set and vector similarity measures. |
| MOUSE_IGHD | Alphabets of TCR and Ig gene segments. |
| MOUSE_IGHJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_IGHV | Alphabets of TCR and Ig gene segments. |
| MOUSE_IGKJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_IGKV | Alphabets of TCR and Ig gene segments. |
| MOUSE_IGLJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_IGLV | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRAJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRAV | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRBJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRBV | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRDD | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRDJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRDV | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRGJ | Alphabets of TCR and Ig gene segments. |
| MOUSE_TRGV | Alphabets of TCR and Ig gene segments. |
| mutated.neighbours | Get vertex neighbours. |
| mutation.network | Make mutation network for the given repertoire. |
| overlap.coef | Set and vector similarity measures. |
| ozScore | Overlap Z-score. |
| parse.cloneset | Parse input table files with the immune receptor repertoire data. |
| parse.file | Parse input table files with immune receptor repertoire data. |
| parse.file.list | Parse input table files with immune receptor repertoire data. |
| parse.folder | Parse input table files with immune receptor repertoire data. |
| parse.immunoseq | Parse input table files with immune receptor repertoire data. |
| parse.immunoseq2 | Parse input table files with immune receptor repertoire data. |
| parse.immunoseq3 | Parse input table files with immune receptor repertoire data. |
| parse.imseq | Parse input table files with immune receptor repertoire data. |
| parse.migec | Parse input table files with immune receptor repertoire data. |
| parse.migmap | Parse input table files with immune receptor repertoire data. |
| parse.mitcr | Parse input table files with immune receptor repertoire data. |
| parse.mitcrbc | Parse input table files with immune receptor repertoire data. |
| parse.mixcr | Parse input table files with immune receptor repertoire data. |
| parse.tcr | Parse input table files with immune receptor repertoire data. |
| parse.vdjtools | Parse input table files with immune receptor repertoire data. |
| pca.segments | Perform PCA on segments frequency data. |
| pca.segments.2D | Perform PCA on segments frequency data. |
| pca2euclid | Compute the Euclidean distance among principal components. |
| permutDistTest | Monte Carlo permutation test for pairwise and one-vs-all-wise within- and inter-group differences in a set of repertoires. |
| permutedf | Shuffling data frames. |
| prop.sample | Resample data frame using values from the column with number of clonesets. |
| rarefaction | Diversity evaluation using rarefaction. |
| repDiversity | General function for the repertoire diversity estimation. |
| repLoad | Parse input files or folders with immune receptor repertoire data. |
| repOverlap | General function for the repertoire overlap evaluation. |
| repSave | Save tcR data frames to disk as text files or gzipped text files. |
| repseq.stats | MiTCR data frame basic statistics. |
| resample | Resample data frame using values from the column with number of clonesets. |
| revcomp | DNA reverse complementing and translation. |
| reverse.string | Reverse given character vector by the given n-plets. |
| reverse.translation | Functions for working with aminoacid sequences. |
| sample.clones | Get a random subset from a data.frame. |
| sample2D | Get a sample from matrix with probabilities. |
| 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.index | Set new columns "Rank" and "Index". |
| set.pb | Simple functions for manipulating progress bars. |
| set.people.vector | Set and get attributes of a mutation network related to source people. |
| set.rank | Set new columns "Rank" and "Index". |
| shared.clones.count | Shared repertoire analysis. |
| shared.matrix | Shared TCR repertoire managing and analysis |
| shared.repertoire | Shared TCR repertoire managing and analysis |
| shared.representation | Shared repertoire analysis. |
| shared.summary | Shared repertoire analysis. |
| similarity | Set and vector similarity measures. |
| slice_fun | Get samples from a repertoire slice-by-slice or top-by-top and apply function to them. |
| 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 frame. |
| top.cross.plot | Perform sequential cross starting from the top of a data frame. |
| top.cross.vec | 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. |
| top.proportion | Proportions of specifyed subsets of clones. |
| translated.nucl.sequences | Functions for working with aminoacid sequences. |
| tversky.index | Set and vector similarity measures. |
| twa | Twins alpha-beta chain data |
| twb | Twins alpha-beta chain data |
| twinsdata | Twins alpha-beta chain data |
| unpermutedf | Shuffling data frames. |
| vis.clonal.dynamics | Visualise clonal dynamics among time points. |
| vis.clonal.space | Visualise occupied by clones homeostatic space among Samples or groups. |
| 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.J.usage | Histogram of segments usage. |
| 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 repertoires. |
| vis.top.proportions | Visualisation of top clones proportions. |
| vis.V.usage | Histogram of segments usage. |
| .add.legend | Internal function. Add legend to a grid of plots and remove legend from all plots of a grid. |
| .column.choice | Choose the right column. |
| .fix.listnames | Fix names in lists. |
| .verbose.msg | Print the given message if second parameter is a TRUE. |