Package index • immunarch

Stable, v1.0

… work in progress …

Experimental, v1.0

Repertoire descriptive statistics

airr_stats_chains() airr_stats_lengths() airr_stats_genes() experimental: Compute key immune repertoire statistics

Clonality

airr_clonality_line() airr_clonality_rank() airr_clonality_prop() experimental: Clonality - receptor overabundance statistics for immune repertoires

annotate_clonality_rank() annotate_clonality_prop() experimental: Annotate clonality - per-receptor labels for overabundance

Diversity

airr_diversity_dxx() airr_diversity_chao1() airr_diversity_shannon() airr_diversity_pielou() airr_diversity_index() airr_diversity_hill() experimental: Diversity - estimating the heterogeneity of immune repertoires

Public indices

airr_public_intersection() airr_public_jaccard() experimental: Public indices - pairwise repertoire overlap

Technical

register_immunarch_method() experimental: Register an Immunarch method (developer)

vis() experimental: One function to visualise them all

aa_properties properties kidera KIDERA aa_prop AA_PROP atchley ATCHLEY: Tables with amino acid properties

AA_TABLE: Amino acid / codon table

bcrdata: BCR dataset

gene_segments genes segments GENE_SEGMENTS: Gene segments table

gene_stats(): WIP

immdata: Single chain immune repertoire dataset

immunr_data_format immunarch_data_format: Specification of the data format used by immunarch dataframes

get_immunarch_news(): Get the Latest immunarch Update

immunarch_v1_updates: Get a list of package updates

list_immunarch_news(): List Available immunarch Updates

Under Question, v0.9 -> v1.0

add_class(): Add a new class attribute

check_distribution(): Check and normalise distributions

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

group_from_metadata(): Get a character vector of samples' groups from the input metadata file

has_class(): Check for the specific class

matrixdiagcopy(): Copy the upper matrix triangle to the lower one

set_pb() add_pb(): Set and update progress bars

switch_type() process_col_argument(): Return a column's name

apply_symm() apply_asymm(): Apply function to each pair of data frames from a list.

entropy() kl_div() js_div() cross_entropy() deprecated: Information measures

bunch_translate(): Nucleotide to amino acid sequence translation

coding() noncoding() inframes() outofframes(): Filter out coding and non-coding clonotype sequences

repSample() deprecated: Downsampling and resampling of immune repertoires

top(): Get the N most abundant clonotypes

Deprecated, v0.9

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

dbLoad() deprecated: Load clonotype databases such as VDJDB and McPAS into the R workspace

entropy() kl_div() js_div() cross_entropy() deprecated: Information measures

fixVis() deprecated: Manipulate ggplot plots and create publication-ready plots

geneUsage() deprecated: Main function for estimation of V-gene and J-gene statistics

geneUsageAnalysis() deprecated: Post-analysis of V-gene and J-gene statistics: PCA, clustering, etc.

getKmers() deprecated: Calculate the k-mer statistics of immune repertoires

immunr_hclust() immunr_kmeans() immunr_dbscan() deprecated: Clustering of objects or distance matrices

immunr_pca() immunr_mds() immunr_tsne() deprecated: Dimensionality reduction

inc_overlap() deprecated: Incremental counting of repertoire similarity

pubRep() deprecated: Create a repertoire of public clonotypes

pubRepApply() deprecated: Apply transformations to public repertoires

pubRepFilter() deprecated: Filter out clonotypes from public repertoires

pubRepStatistics() deprecated: Statistics of number of public clonotypes for each possible combinations of repertoires

public_matrix() deprecated: Get a matrix with public clonotype frequencies

repAlignLineage() deprecated: Aligns all sequences incliding germline within each clonal lineage within each cluster

repClonalFamily() deprecated: Builds a phylogenetic tree using the sequences of a clonal lineage

repClonality() deprecated: Clonality analysis of immune repertoires

repDiversity() deprecated: The main function for immune repertoire diversity estimation

repExplore() deprecated: Main function for exploratory data analysis: compute the distribution of lengths, clones, etc.

repFilter() deprecated: Main function for data filtering

repGermline() deprecated: Creates germlines for clonal lineages

repLoad() deprecated: Load immune repertoire files into the R workspace

repOverlap() deprecated: Main function for public clonotype statistics calculations

repOverlapAnalysis() deprecated: Post-analysis of public clonotype statistics: PCA, clustering, etc.

repSample() deprecated: Downsampling and resampling of immune repertoires

repSave() deprecated: Save immune repertoires to the disk

repSomaticHypermutation() deprecated: Calculates number of mutations against the germline for each clonotype

select_barcodes() deprecated: Select specific clonotypes using barcodes from single-cell metadata

select_clusters() deprecated: Split the immune repertoire data to clusters from single-cell barcodes

seqCluster() deprecated: Function for assigning clusters based on sequences similarity

seqDist() deprecated: Function for computing distance for sequences

spectratype() deprecated: Immune repertoire spectratyping

split_to_kmers() kmer_profile() deprecated: Analysis immune repertoire kmer statistics: sequence profiles, etc.

trackClonotypes() deprecated: Track clonotypes across time and data points

vis(<clonal_family>) deprecated: Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output

vis(<clonal_family_tree>) deprecated: Visualise clonal family tree

vis(<immunr_chao1>) deprecated: Visualise diversity.

vis(<immunr_clonal_prop>) deprecated: Visualise results of the clonality analysis

vis(<immunr_dynamics>) deprecated: Visualise clonotype dynamics

vis(<immunr_exp_vol>) deprecated: Visualise results of the exploratory analysis

vis(<immunr_gene_usage>) deprecated: Histograms and boxplots (general case / gene usage)

vis(<immunr_hclust>) deprecated: Visualisation of hierarchical clustering

vis(<immunr_inc_overlap>) deprecated: Visualise incremental overlaps

vis(<immunr_kmeans>) deprecated: Visualisation of K-means and DBSCAN clustering

vis(<immunr_kmer_table>) deprecated: Most frequent kmers visualisation.

vis(<immunr_mds>) deprecated: PCA / MDS / tSNE visualisation (mainly overlap / gene usage)

vis(<immunr_ov_matrix>) deprecated: Repertoire overlap and gene usage visualisations

vis(<immunr_public_repertoire>) deprecated: Public repertoire visualisation

vis(<immunr_public_statistics>) deprecated: Visualise sharing of clonotypes among samples

vis(<step_failure_ignored>) deprecated: Handler for .nofail argument of pipeline steps that prevents examples from crashing on computers where certain dependencies are not installed

vis_bar() deprecated: Bar plots

vis_box() deprecated: Flexible box-plots for visualisation of distributions

vis_circos() deprecated: Visualisation of matrices using circos plots

vis_heatmap() deprecated: Visualisation of matrices and data frames using ggplo2-based heatmaps

vis_heatmap2() deprecated: Visualisation of matrices using pheatmap-based heatmaps

vis_hist() deprecated: Visualisation of distributions using histograms

vis_immunr_kmer_profile_main() deprecated: Visualise kmer profiles

vis_public_clonotypes() deprecated: Visualisation of public clonotypes

vis_public_frequencies() deprecated: Public repertoire visualisation

vis_textlogo() vis_seqlogo() deprecated: Sequence logo plots for amino acid profiles.