All functions

aa_properties

Tables with amino acid properties

AA_TABLE

Amino acid / codon table

add_class()

Add a new class attribute to the input object.

apply.symm() apply.asymm()

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

bunch_translate()

Translate

cdrProp()

AA properties calculation

check_distribution()

Check that distribution is sums up to one.

check_group_names()

Check if everything is ok with group names

coding()

Work in progress

.make_names()

Additional functions for help in parsing

entropy()

Information measures

fixVis()

Make publication-ready plots

geneUsage()

Gene usage

geneUsageAnalysis()

Analysis of gene usage

gene_segments

Gene segments table.

gene_stats()

WIP

getKmers()

Kmer analysis of repertoires.

get_rank()

Get ranks / indices for counts of clonotypes

gibbs_sampling()

Simple Gibbs sampling on kmers.

group_from_metadata()

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

has_class()

Check class

immunr_data_format

Specification of the data format used by immunarch dataframes.

immunr_hclust() immunr_kmeans() immunr_dbscan()

Clustering of objects or distance matrices

immunr_pca() immunr_mds() immunr_tsne()

Dimensionality reduction

immunr_permut()

Statistical analysis of groups

kmerAnalysis()

WIP

load_test_data()

Various functions for testing purposes

lookup_clonotypes()

Search for clonotypes in external databases

num_shared_clonotypes()

Number of shared clonotypes.

overlap_coef() jaccard_index() tversky_index() cosine_sim() morisita_index() horn_index()

Various measures for overlapping sets of objects.

repClonality()

Assess clonal proportions of repertoire

repDiversity()

Estimate diversity of repertoire

repExplore()

Explore basics of repertoire

repLoad()

Load repertoire files to the workspace

repOverlap()

Calculate the overlap between repertoires

repOverlapAnalysis()

Analysis of overlaps or any distance matrices

repSave()

Save repertoire files to the disk.

resample() downsample() prop_sample()

Resample data frame using values from the column with number of clonesets.

set_pb()

Set and update progress bars

spectratype()

Analyse spectratype of immune repertoire

split_immunoseq_files()

Split all-samples-in-one ImmunoSEQ files by sample

split_to_kmers()

Kmers processing.

switch_type()

WIP

top()

Work in progress

top_overlap()

Sequential overlap of top-by-count clonotypes.

trackClonotypes() tr.clo() poisson_model() norm_model()

Clonotype tracking across different samples.

vis

One function to visualise them all

vis.immunr_cdr_prop

Work in progress

vis.immunr_chao1

Visualise diversity.

vis.immunr_clonal_prop

Visualise clonality

vis.immunr_dynamics

Repertoire dynamics

vis.immunr_exp_vol

Visualise exploratory analysis.

vis.immunr_gene_usage

Histograms and boxplots (general case / gene usage)

vis.immunr_hclust() vis.immunr_kmeans() vis.immunr_dbscan()

Visualisation of clustering results

vis.immunr_kmer_table

Most frequent kmers visualisation.

vis.immunr_mds

PCA / MDS / tSNE visualisation (mainly overlap / gene usage)

vis.immunr_mutation_network

Work in progress

vis.immunr_ov_matrix

Overlap / gene usage distance visualisation

vis.immunr_public_repertoire

Public repertoire visualisation

vis.immunr_top_overlap

Visualise incremental overlaps

vis_box

Visualisation of distributions using boxplots

vis_circos

Visualisation of matrices using circos plots

vis_heatmap

Visualisation of matrices and data frames using ggplot2-based heatmaps

vis_heatmap2

Visualisation of matrices using heatmap3-based heatmaps

vis_hist

Visualisation of distributions using histograms

vis_logo

Logo - plots for amino acid and nucletide profiles.

vis_radar

Visualisation of distance matrices with polar area plots

vis_treemap

Visualisation of data frames and matrices using treemaps