immunarch0.10.3 package

Tables with amino acid properties

Amino acid / codon table

Add a new class attribute

Clonality - receptor overabundance statistics for immune repertoires

Diversity - estimating the heterogeneity of immune repertoires

Public indices - pairwise repertoire overlap

Compute key immune repertoire statistics

Annotate clonality - per-receptor labels for overabundance

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

Nucleotide to amino acid sequence translation

Check and normalise distributions

Filter out coding and non-coding clonotype sequences

Annotate clonotypes in immune repertoires using clonotype databases (e...

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

Get a column's name using the input alias

Information measures

Manipulate ggplot plots and create publication-ready plots

Gene segments table

WIP

Main function for estimation of V-gene and J-gene statistics

Post-analysis of V-gene and J-gene statistics: PCA, clustering, etc.

Get the Latest immunarch Update

Calculate the k-mer statistics of immune repertoires

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

Check for the specific class

Common arguments for immunarch helpers

Get a list of package updates

Specification of the data format used by immunarch dataframes

Clustering of objects or distance matrices

Dimensionality reduction

Incremental counting of repertoire similarity

List Available immunarch Updates

Copy the upper matrix triangle to the lower one

Get a matrix with public clonotype frequencies

Create a repertoire of public clonotypes

Apply transformations to public repertoires

Filter out clonotypes from public repertoires

Statistics of number of public clonotypes for each possible combinatio...

Register an Immunarch method (developer)

Aligns all sequences incliding germline within each clonal lineage wit...

Builds a phylogenetic tree using the sequences of a clonal lineage

Clonality analysis of immune repertoires

The main function for immune repertoire diversity estimation

Main function for exploratory data analysis: compute the distribution ...

Main function for data filtering

Creates germlines for clonal lineages

Load immune repertoire files into the R workspace

Main function for public clonotype statistics calculations

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

Downsampling and resampling of immune repertoires

Save immune repertoires to the disk

Calculates number of mutations against the germline for each clonotype

Select specific clonotypes using barcodes from single-cell metadata

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

Function for assigning clusters based on sequences similarity

Function for computing distance for sequences

Set and update progress bars

Immune repertoire spectratyping

Analysis immune repertoire kmer statistics: sequence profiles, etc.

Return a column's name

Get the N most abundant clonotypes

Track clonotypes across time and data points

Bar plots

Flexible box-plots for visualisation of distributions

Visualisation of matrices using circos plots

Visualisation of matrices and data frames using ggplo2-based heatmaps

Visualisation of matrices using pheatmap-based heatmaps

Visualisation of distributions using histograms

Visualise kmer profiles

Visualisation of public clonotypes

Public repertoire visualisation

Sequence logo plots for amino acid profiles.

Visualise clonal family tree

Visualise clonal family tree: wrapper for calling on the entire repClo...

Visualise diversity.

Visualise results of the clonality analysis

Visualise clonotype dynamics

Visualise results of the exploratory analysis

Histograms and boxplots (general case / gene usage)

Visualisation of hierarchical clustering

Visualise incremental overlaps

Visualisation of K-means and DBSCAN clustering

Most frequent kmers visualisation.

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

Repertoire overlap and gene usage visualisations

Public repertoire visualisation

Visualise sharing of clonotypes among samples

One function to visualise them all

Handler for .nofail argument of pipeline steps that prevents examples ...