A B C D E F G H I J K L M O P R S T U V
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. |
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. |