Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

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Documentation for package ‘immunarch’ version 0.9.1

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A B C D E F G H I J K L M N O P R S T V misc

-- A --

AA_PROP Tables with amino acid properties
aa_prop Tables with amino acid properties
aa_properties Tables with amino acid properties
AA_TABLE Amino acid / codon table
aa_table Amino acid / codon table
AA_TABLE_REVERSED Amino acid / codon table
add_class Add a new class attribute
add_pb Set and update progress bars
apply_asymm Apply function to each pair of data frames from a list.
apply_symm Apply function to each pair of data frames from a list.
ATCHLEY Tables with amino acid properties
atchley Tables with amino acid properties

-- B --

bcrdata BCR dataset
bunch_translate Nucleotide to amino acid sequence translation

-- C --

chao1 The main function for immune repertoire diversity estimation
check_distribution Check and normalise distributions
clonal.prop Clonality analysis of immune repertoires
clonality Clonality analysis of immune repertoires
clonal_proportion Clonality analysis of immune repertoires
clonal_space_homeostasis Clonality analysis of immune repertoires
coding Filter out coding and non-coding clonotype sequences
cross_entropy Information measures

-- D --

dbAnnotate Annotate clonotypes in immune repertoires using clonotype databases such as VDJDB and MCPAS
dbLoad Load clonotype databases such as VDJDB and McPAS into the R workspace
diversity_eco The main function for immune repertoire diversity estimation

-- E --

entropy Information measures
exclude Main function for data filtering

-- F --

fixVis Manipulate ggplot plots and create publication-ready plots

-- G --

genes Gene segments table
geneUsage Main function for estimation of V-gene and J-gene statistics
geneUsageAnalysis Post-analysis of V-gene and J-gene statistics: PCA, clustering, etc.
GENE_SEGMENTS Gene segments table
gene_segments Gene segments table
gene_stats WIP
get.kmers Calculate the k-mer statistics of immune repertoires
getKmers Calculate the k-mer statistics of immune repertoires
get_aliases Main function for estimation of V-gene and J-gene statistics
get_genes Main function for estimation of V-gene and J-gene statistics
gini_coef The main function for immune repertoire diversity estimation
gini_simpson The main function for immune repertoire diversity estimation
group_from_metadata Get a character vector of samples' groups from the input metadata file

-- H --

has_class Check for the specific class
hill_numbers The main function for immune repertoire diversity estimation

-- I --

immdata Single chain immune repertoire dataset
immunarch_data_format Specification of the data format used by immunarch dataframes
immunr_data_format Specification of the data format used by immunarch dataframes
immunr_dbscan Clustering of objects or distance matrices
immunr_hclust Clustering of objects or distance matrices
immunr_kmeans Clustering of objects or distance matrices
immunr_mds Dimensionality reduction
immunr_pca Dimensionality reduction
immunr_tsne Dimensionality reduction
include Main function for data filtering
inc_overlap Incremental counting of repertoire similarity
inframes Filter out coding and non-coding clonotype sequences
interval Main function for data filtering
inverse_simpson The main function for immune repertoire diversity estimation

-- J --

js_div Information measures

-- K --

KIDERA Tables with amino acid properties
kidera Tables with amino acid properties
kl_div Information measures
kmer_profile Analysis immune repertoire kmer statistics: sequence profiles, etc.

-- L --

lessthan Main function for data filtering

-- M --

makeKmerTable Calculate the k-mer statistics of immune repertoires
matrixdiagcopy Copy the upper matrix triangle to the lower one
morethan Main function for data filtering

-- N --

noncoding Filter out coding and non-coding clonotype sequences

-- O --

outofframes Filter out coding and non-coding clonotype sequences

-- P --

process_col_argument Return a column's name
properties Tables with amino acid properties
publicRepertoire Create a repertoire of public clonotypes
publicRepertoireApply Apply transformations to public repertoires
publicRepertoireFilter Filter out clonotypes from public repertoires
public_matrix Get a matrix with public clonotype frequencies
pubRep Create a repertoire of public clonotypes
pubRepApply Apply transformations to public repertoires
pubRepFilter Filter out clonotypes from public repertoires
pubRepStatistics Statistics of number of public clonotypes for each possible combinations of repertoires

-- R --

rarefaction The main function for immune repertoire diversity estimation
rare_proportion Clonality analysis of immune repertoires
repAlignLineage Aligns all sequences incliding germline within each clonal lineage within each cluster
repClonalFamily Builds a phylogenetic tree using the sequences of a clonal lineage
repClonality Clonality analysis of immune repertoires
repDiversity The main function for immune repertoire diversity estimation
repExplore Main function for exploratory data analysis: compute the distribution of lengths, clones, etc.
repFilter Main function for data filtering
repGermline Creates germlines for clonal lineages
repLoad Load immune repertoire files into the R workspace
repOverlap Main function for public clonotype statistics calculations
repOverlapAnalysis Post-analysis of public clonotype statistics: PCA, clustering, etc.
repSample Downsampling and resampling of immune repertoires
repSave Save immune repertoires to the disk
repSomaticHypermutation Calculates number of mutations against the germline for each clonotype

-- S --

scdata Paired chain immune repertoire dataset
segments Gene segments table
select_barcodes Select specific clonotypes using barcodes from single-cell metadata
select_clusters Split the immune repertoire data to clusters from single-cell barcodes
seqCluster Function for assigning clusters based on sequences similarity
seqDist Function for computing distance for sequences
set_pb Set and update progress bars
spectratype Immune repertoire spectratyping
split_to_kmers Analysis immune repertoire kmer statistics: sequence profiles, etc.
switch_type Return a column's name

-- T --

top Get the N most abundant clonotypes
top_proportion Clonality analysis of immune repertoires
trackClonotypes Track clonotypes across time and data points
translate_bunch Nucleotide to amino acid sequence translation

-- V --

vis One function to visualise them all
vis.clonal_family Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output
vis.clonal_family_tree Visualise clonal family tree
vis.immunr_chao1 Visualise diversity.
vis.immunr_clonal_prop Visualise results of the clonality analysis
vis.immunr_dbscan Visualisation of K-means and DBSCAN clustering
vis.immunr_div Visualise diversity.
vis.immunr_dxx Visualise diversity.
vis.immunr_dynamics Visualise clonotype dynamics
vis.immunr_exp_clones Visualise results of the exploratory analysis
vis.immunr_exp_count Visualise results of the exploratory analysis
vis.immunr_exp_len Visualise results of the exploratory analysis
vis.immunr_exp_vol Visualise results of the exploratory analysis
vis.immunr_gene_usage Histograms and boxplots (general case / gene usage)
vis.immunr_ginisimp Visualise diversity.
vis.immunr_gu_matrix Repertoire overlap and gene usage visualisations
vis.immunr_hclust Visualisation of hierarchical clustering
vis.immunr_hill Visualise diversity.
vis.immunr_homeo Visualise results of the clonality analysis
vis.immunr_inc_overlap Visualise incremental overlaps
vis.immunr_invsimp Visualise diversity.
vis.immunr_kmeans Visualisation of K-means and DBSCAN clustering
vis.immunr_kmer_table Most frequent kmers visualisation.
vis.immunr_mds PCA / MDS / tSNE visualisation (mainly overlap / gene usage)
vis.immunr_ov_matrix Repertoire overlap and gene usage visualisations
vis.immunr_pca PCA / MDS / tSNE visualisation (mainly overlap / gene usage)
vis.immunr_public_repertoire Public repertoire visualisation
vis.immunr_public_statistics Visualise sharing of clonotypes among samples
vis.immunr_rarefaction Visualise diversity.
vis.immunr_tail_prop Visualise results of the clonality analysis
vis.immunr_top_prop Visualise results of the clonality analysis
vis.immunr_tsne PCA / MDS / tSNE visualisation (mainly overlap / gene usage)
vis.step_failure_ignored Handler for .nofail argument of pipeline steps that prevents examples from crashing on computers where certain dependencies are not installed
vis_bar Bar plots
vis_box Flexible box-plots for visualisation of distributions
vis_circos Visualisation of matrices using circos plots
vis_heatmap Visualisation of matrices and data frames using ggplo2-based heatmaps
vis_heatmap2 Visualisation of matrices using pheatmap-based heatmaps
vis_hist Visualisation of distributions using histograms
vis_immunr_kmer_profile_main Visualise kmer profiles
vis_public_clonotypes Visualisation of public clonotypes
vis_public_frequencies Public repertoire visualisation
vis_seqlogo Sequence logo plots for amino acid profiles.
vis_textlogo Sequence logo plots for amino acid profiles.

-- misc --

.quant_column_choice Get a column's name using the input alias