Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Tables with amino acid properties
Amino acid / codon table
Add a new class attribute
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 su...
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.
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
Specification of the data format used by immunarch dataframes
Clustering of objects or distance matrices
Dimensionality reduction
Incremental counting of repertoire similarity
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...
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
Visualise clonal family tree: wrapper for calling on the entire repClo...
Visualise clonal family tree
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 ...
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.
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Useful links