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()

Nucleotide to amino acid sequence translation

check_distribution()

Check that distribution is sums up to one.

coding() noncoding() inframes() outofframes()

Working with coding and non-coding clonotype sequences

.quant_column_choice()

Get a column's name using the input alias

entropy() kl_div() js_div() cross_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.

group_from_metadata()

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

has_class()

Check class

immdata

Immune repertoire dataset

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

inc_overlap()

Incremental counting of repertoire similarity

lookup_clonotypes()

Search for clonotypes in external databases

matrixdiagcopy()

Copy the upper matrix triangle to the lower one

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.

pubRep()

Public repertoire

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

public_matrix()

Get a matrix with public clonotype frequencies

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

repSample()

Sampling of repertoires

repSave()

Save repertoire files to the disk.

set_pb() add_pb()

Set and update progress bars

spectratype()

Analyse spectratype of immune repertoires

split_immunoseq_files()

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

split_to_kmers() kmer_profile()

Kmers processing.

switch_type() process_col_argument()

Return a column's name

top()

Get the N most abundant clonotypes

trackClonotypes()

Clonotype tracking

vis()

One function to visualise them all

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>)

Visualisation of hierarchical clustering

vis(<immunr_inc_overlap>)

Visualise incremental overlaps

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>)

Overlap / gene usage distance visualisation

vis(<immunr_public_repertoire>)

Public repertoire visualisation

vis(<immunr_public_statistics>)

Visualise sharing of clonotypes among samples

vis_bar()

Bar plots

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_immunr_kmer_profile_main()

Visualise kmer profiles

vis_public_clonotypes()

Visualisation of public clonotypes

vis_public_frequencies()

Public repertoire visualisation

vis_radar()

Visualisation of distance matrices with polar area plots

vis_textlogo() vis_seqlogo()

Sequence logo plots for amino acid profiles.

vis_treemap()

Visualisation of data frames and matrices using treemaps