Man pages for immunarch
Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

aa_propertiesTables with amino acid properties
aa_tableAmino acid / codon table
add_classAdd a new class attribute
apply_symmApply function to each pair of data frames from a list.
bunch_translateNucleotide to amino acid sequence translation
check_distributionCheck and normalise distributions
codingFilter out coding and non-coding clonotype sequences
dbAnnotateAnnotate clonotypes in immune repertoires using clonotype...
dbLoadLoad clonotype databases such as VDJDB and McPAS into the R...
dot-quant_column_choiceGet a column's name using the input alias
entropyInformation measures
fixVisManipulate ggplot plots and make publication-ready plots
gene_segmentsGene segments table
geneUsageMain function for estimation of V-gene and J-gene statistics
geneUsageAnalysisPost-analysis of V-gene and J-gene statistics: PCA,...
getKmersCalculate the kmer statistics of immune repertoires
group_from_metadataGet a character vector of samples' groups from the input...
has_classCheck for the specific class
immdataSingle chain immune repertoire dataset
immunr_data_formatSpecification of the data format used by immunarch dataframes
immunr_hclustClustering of objects or distance matrices
immunr_pcaDimensionality reduction
inc_overlapIncremental counting of repertoire similarity
matrixdiagcopyCopy the upper matrix triangle to the lower one
public_matrixGet a matrix with public clonotype frequencies
pubRepCreate a repertoire of public clonotypes
pubRepApplyApply transformations to public repertoires
pubRepFilterFilter out clonotypes from public repertoires
pubRepStatisticsStatistics of number of public clonotypes for each possible...
repClonalityClonality analysis of immune repertoires
repDiversityMain function for immune repertoire diversity estimation
repExploreMain function for exploratory data analysis: compute the...
repLoadLoad immune repertoire files into the R workspace
repOverlapMain function for public clonotype statistics calculations
repOverlapAnalysisPost-analysis of public clonotype statistics: PCA,...
repSampleDownsampling and resampling of immune repertoires
repSaveSave immune repertoires to the disk
scdataPaired chain immune repertoire dataset
select_barcodesSelect specific clonotypes using barcodes from single-cell...
select_clustersSplit the immune repertoire data to clusters from single-cell...
set_pbSet and update progress bars
spectratypeImmune repertoire spectratyping
split_to_kmersAnalysis immune repertoire kmer statistics: sequence...
switch_typeReturn a column's name
topGet the N most abundant clonotypes
trackClonotypesTrack clonotypes across time and data points
visOne function to visualise them all
vis_barBar plots
vis_boxFlexible box-plots for visualisation of distributions
vis_circosVisualisation of matrices using circos plots
vis_heatmapVisualisation of matrices and data frames using ggplo2-based...
vis_heatmap2Visualisation of matrices using pheatmap-based heatmaps
vis_histVisualisation of distributions using histograms
vis.immunr_chao1Visualise diversity.
vis.immunr_clonal_propVisualise results of the clonality analysis
vis.immunr_dynamicsVisualise clonotype dynamics
vis.immunr_exp_volVisualise results of the exploratory analysis
vis.immunr_gene_usageHistograms and boxplots (general case / gene usage)
vis.immunr_hclustVisualisation of hierarchical clustering
vis.immunr_inc_overlapVisualise incremental overlaps
vis.immunr_kmeansVisualisation of K-means and DBSCAN clustering
vis_immunr_kmer_profile_mainVisualise kmer profiles
vis.immunr_kmer_tableMost frequent kmers visualisation.
vis.immunr_mdsPCA / MDS / tSNE visualisation (mainly overlap / gene usage)
vis.immunr_ov_matrixRepertoire overlap and gene usage visualisations
vis.immunr_public_repertoirePublic repertoire visualisation
vis.immunr_public_statisticsVisualise sharing of clonotypes among samples
vis_public_clonotypesVisualisation of public clonotypes
vis_public_frequenciesPublic repertoire visualisation
vis_textlogoSequence logo plots for amino acid profiles.
immunarch documentation built on July 7, 2021, 9:08 a.m.