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install.packages('immunarch')

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5,520

Version

0.10.3

License

Apache License (>= 2.0)

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3

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1

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327

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71

Maintainer

Vadim I. Nazarov

Last Published

October 15th, 2025

Functions in immunarch (0.10.3)

immunarch_v1_updates

Get a list of package updates
.quant_column_choice

Get a column's name using the input alias
pubRep

Create a repertoire of public clonotypes
matrixdiagcopy

Copy the upper matrix triangle to the lower one
immunr_data_format

Specification of the data format used by immunarch dataframes
gene_segments

Gene segments table
gene_stats

WIP
public_matrix

Get a matrix with public clonotype frequencies
pubRepStatistics

Statistics of number of public clonotypes for each possible combinations of repertoires
pubRepApply

Apply transformations to public repertoires
pubRepFilter

Filter out clonotypes from public repertoires
immunr_pca

Dimensionality reduction
immunr_hclust

Clustering of objects or distance matrices
im_common_args

Common arguments for immunarch helpers
repLoad

Load immune repertoire files into the R workspace
group_from_metadata

Get a character vector of samples' groups from the input metadata file
has_class

Check for the specific class
list_immunarch_news

List Available immunarch Updates
inc_overlap

Incremental counting of repertoire similarity
repSample

Downsampling and resampling of immune repertoires
repOverlapAnalysis

Post-analysis of public clonotype statistics: PCA, clustering, etc.
repClonalFamily

Builds a phylogenetic tree using the sequences of a clonal lineage
immdata

Single chain immune repertoire dataset
getKmers

Calculate the k-mer statistics of immune repertoires
repExplore

Main function for exploratory data analysis: compute the distribution of lengths, clones, etc.
select_clusters

Split the immune repertoire data to clusters from single-cell barcodes
repDiversity

The main function for immune repertoire diversity estimation
select_barcodes

Select specific clonotypes using barcodes from single-cell metadata
seqDist

Function for computing distance for sequences
repAlignLineage

Aligns all sequences incliding germline within each clonal lineage within each cluster
register_immunarch_method

Register an Immunarch method (developer)
repOverlap

Main function for public clonotype statistics calculations
top

Get the N most abundant clonotypes
vis.clonal_family_tree

Visualise clonal family tree
vis.immunr_hclust

Visualisation of hierarchical clustering
vis.immunr_chao1

Visualise diversity.
seqCluster

Function for assigning clusters based on sequences similarity
vis.immunr_public_statistics

Visualise sharing of clonotypes among samples
vis.immunr_public_repertoire

Public repertoire visualisation
repFilter

Main function for data filtering
get_immunarch_news

Get the Latest immunarch Update
vis.immunr_kmer_table

Most frequent kmers visualisation.
vis_immunr_kmer_profile_main

Visualise kmer profiles
trackClonotypes

Track clonotypes across time and data points
vis_textlogo

Sequence logo plots for amino acid profiles.
vis_hist

Visualisation of distributions using histograms
vis.immunr_kmeans

Visualisation of K-means and DBSCAN clustering
repClonality

Clonality analysis of immune repertoires
set_pb

Set and update progress bars
vis_public_clonotypes

Visualisation of public clonotypes
repGermline

Creates germlines for clonal lineages
vis.immunr_inc_overlap

Visualise incremental overlaps
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

One function to visualise them all
vis_circos

Visualisation of matrices using circos plots
vis_box

Flexible box-plots for visualisation of distributions
vis.immunr_clonal_prop

Visualise results of the clonality analysis
repSave

Save immune repertoires to the disk
repSomaticHypermutation

Calculates number of mutations against the germline for each clonotype
vis.immunr_mds

PCA / MDS / tSNE visualisation (mainly overlap / gene usage)
vis.clonal_family

Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output
vis.immunr_ov_matrix

Repertoire overlap and gene usage visualisations
vis.immunr_dynamics

Visualise clonotype dynamics
split_to_kmers

Analysis immune repertoire kmer statistics: sequence profiles, etc.
spectratype

Immune repertoire spectratyping
vis.immunr_exp_vol

Visualise results of the exploratory analysis
switch_type

Return a column's name
vis.immunr_gene_usage

Histograms and boxplots (general case / gene usage)
vis_public_frequencies

Public repertoire visualisation
vis_heatmap

Visualisation of matrices and data frames using ggplo2-based heatmaps
vis_heatmap2

Visualisation of matrices using pheatmap-based heatmaps
aa_properties

Tables with amino acid properties
add_class

Add a new class attribute
aa_table

Amino acid / codon table
airr_stats

Compute key immune repertoire statistics
airr_clonality

Clonality - receptor overabundance statistics for immune repertoires
coding

Filter out coding and non-coding clonotype sequences
dbAnnotate

Annotate clonotypes in immune repertoires using clonotype databases (e.g., VDJDB, McPAS)
annotate_clonality

Annotate clonality - per-receptor labels for overabundance
bunch_translate

Nucleotide to amino acid sequence translation
check_distribution

Check and normalise distributions
entropy

Information measures
fixVis

Manipulate ggplot plots and create publication-ready plots
apply_symm

Apply function to each pair of data frames from a list.
bcrdata

BCR dataset
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.
airr_public

Public indices - pairwise repertoire overlap
airr_diversity

Diversity - estimating the heterogeneity of immune repertoires
dbLoad

Load clonotype databases such as VDJDB and McPAS into the R workspace