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

## Documentation for package ‘immunarch’ version 0.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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