API for tcR
Advanced Data Analysis of Immune Receptor Repertoires
| Global functions | |
|---|---|
| .add.legend | Man page |
| .colourblind.vector | Source code |
| .column.choice | Man page |
| .exact_search | Source code |
| .exact_search_list | Source code |
| .fix.listnames | Man page |
| .hamming_search | Source code |
| .levenshtein_search | Source code |
| .onAttach | Source code |
| .verbose.msg | Man page |
| AA_TABLE | Man page |
| AA_TABLE_REVERSED | Man page |
| HUMAN_IGHD | Man page |
| HUMAN_IGHJ | Man page |
| HUMAN_IGHV | Man page |
| HUMAN_IGKJ | Man page |
| HUMAN_IGKV | Man page |
| HUMAN_IGLJ | Man page |
| HUMAN_IGLV | Man page |
| HUMAN_TRAJ | Man page |
| HUMAN_TRAV | Man page |
| HUMAN_TRBD | Man page |
| HUMAN_TRBJ | Man page |
| HUMAN_TRBV | Man page |
| HUMAN_TRBV_ALS | Man page |
| HUMAN_TRBV_FAM | Man page |
| HUMAN_TRBV_GEN | Man page |
| HUMAN_TRBV_MITCR | Man page |
| HUMAN_TRDD | Man page |
| HUMAN_TRDJ | Man page |
| HUMAN_TRDV | Man page |
| HUMAN_TRGJ | Man page |
| HUMAN_TRGV | Man page |
| MACMUL_TRBJ | Man page |
| MACMUL_TRBV | Man page |
| MOUSE_IGHD | Man page |
| MOUSE_IGHJ | Man page |
| MOUSE_IGHV | Man page |
| MOUSE_IGKJ | Man page |
| MOUSE_IGKV | Man page |
| MOUSE_IGLJ | Man page |
| MOUSE_IGLV | Man page |
| MOUSE_TRAJ | Man page |
| MOUSE_TRAV | Man page |
| MOUSE_TRBJ | Man page |
| MOUSE_TRBV | Man page |
| MOUSE_TRDD | Man page |
| MOUSE_TRDJ | Man page |
| MOUSE_TRDV | Man page |
| MOUSE_TRGJ | Man page |
| MOUSE_TRGV | Man page |
| add.pb | Man page |
| apply.asymm | Man page |
| apply.symm | Man page |
| assymetry | Man page Source code |
| barcodes.to.reads | Man page |
| beta.prob | Man page |
| bootstrap.tcr | Man page |
| bunch.translate | Man page Source code |
| chao1 | Man page |
| check.distribution | Man page |
| clonal.proportion | Man page |
| clonal.space.homeostasis | Man page |
| cloneset.stats | Man page |
| clonotypescount | Man page Source code |
| codon.variants | Man page |
| column.summary | Man page |
| contamination.stats | Man page |
| convergence.index | Man page |
| cosine.sharing | Man page |
| cosine.similarity | Man page |
| count.frames | Man page |
| count.inframes | Man page |
| count.outframes | Man page |
| decontamination | Man page |
| diversity | Man page |
| downsample | Man page |
| entropy | Man page |
| entropy.seg | Man page |
| exact.match | Man page |
| find.clonotypes | Man page |
| find.similar.sequences | Man page |
| fix.alleles | Man page |
| fix.genes | Man page |
| gc.content | Man page |
| geneUsage | Man page |
| genealphabets | Man page |
| generate.kmers | Man page |
| generate.kmers.prob | Man page |
| generate.tcr | Man page |
| genesegments | Man page |
| get.all.substrings | Man page |
| get.deletions.alpha | Man page |
| get.deletions.beta | Man page |
| get.frames | Man page |
| get.group.names | Man page |
| get.inframes | Man page |
| get.kmer.column | Man page |
| get.kmers | Man page |
| get.outframes | Man page |
| get.people.names | Man page |
| gibbs.sampler | Man page |
| gini | Man page |
| gini.simpson | Man page |
| group.clonotypes | Man page |
| hamming.match | Man page |
| has.class | Man page |
| horn.index | Man page |
| insertion.stats | Man page |
| intersectClonesets | Man page |
| intersectCount | Man page |
| intersectIndices | Man page |
| intersectLogic | Man page |
| inverse.simpson | Man page |
| jaccard.index | Man page |
| js.div | Man page |
| js.div.seg | Man page |
| kl.div | Man page |
| kmer.profile | Man page |
| kmer.table | Man page |
| kmers.profile | Man page |
| levenshtein.match | Man page |
| loglikelihood | Man page |
| matrixSubgroups | Man page |
| matrixdiagcopy | Man page Source code |
| morisitas.index | Man page |
| mutated.neighbours | Man page |
| mutation.network | Man page |
| overlap.coef | Man page |
| ozScore | Man page |
| parse.cloneset | Man page |
| parse.file | Man page Source code |
| parse.file.list | Man page |
| parse.folder | Man page |
| parse.immunoseq | Man page |
| parse.immunoseq2 | Man page |
| parse.immunoseq3 | Man page |
| parse.imseq | Man page |
| parse.migec | Man page |
| parse.migmap | Man page |
| parse.mitcr | Man page |
| parse.mitcrbc | Man page |
| parse.mixcr | Man page |
| parse.tcr | Man page |
| parse.vdjtools | Man page |
| pca.segments | Man page Source code |
| pca.segments.2D | Man page Source code |
| pca2euclid | Man page |
| permutDistTest | Man page |
| permutedf | Man page |
| prop.sample | Man page |
| rarefaction | Man page |
| repDiversity | Man page |
| repLoad | Man page |
| repOverlap | Man page |
| repSave | Man page |
| repseq.stats | Man page Source code |
| resample | Man page |
| revcomp | Man page |
| reverse.string | Man page |
| reverse.translation | Man page |
| sample.clones | Man page |
| sample2D | Man page |
| segments.alphabets | Man page |
| segments.list | Man page |
| set.group.vector | Man page |
| set.index | Man page |
| set.pb | Man page |
| set.people.vector | Man page |
| set.rank | Man page |
| shared.clones.count | Man page |
| shared.matrix | Man page |
| shared.repertoire | Man page |
| shared.representation | Man page |
| shared.summary | Man page |
| similarity | Man page |
| slice_fun | Man page Source code |
| spectratype | Man page |
| startmitcr | Man page |
| tailbound.proportion | Man page |
| top.cross | Man page |
| top.cross.plot | Man page |
| top.cross.vec | Man page |
| top.fun | Man page |
| top.proportion | Man page |
| translated.nucl.sequences | Man page |
| tversky.index | Man page |
| twa | Man page |
| twb | Man page |
| twinsdata | Man page |
| unpermutedf | Man page |
| vis.J.usage | Man page |
| vis.V.usage | Man page |
| vis.clonal.dynamics | Man page |
| vis.clonal.space | Man page |
| vis.count.len | Man page |
| vis.gene.usage | Man page |
| vis.group.boxplot | Man page |
| vis.heatmap | Man page |
| vis.kmer.histogram | Man page |
| vis.logo | Man page |
| vis.number.count | Man page |
| vis.pca | Man page |
| vis.radarlike | Man page |
| vis.rarefaction | Man page |
| vis.shared.clonotypes | Man page |
| vis.top.proportions | Man page |
