scdata

A dataset with paired chain IG data for testing and examplatory purposes.

datasets

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>.

Vadim I. Nazarov

immunarch

Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Vasily O. Tsvetkov

Siarhei Fiadziushchanka

Eugene Rumynskiy

Aleksandr A. Popov

Ivan Balashov

Maria Samokhina

Anna Lorenc

Daniel J. Moore

Victor Greiff

ImmunoMind 

scdata function

A list of four elements:
"data" is a list with data frames with clonotype tables.
"meta" is a metadata table.
"bc_patients" is a list of barcodes corresponding to specific patients.
"bc_clusters" is a list of barcodes corresponding to specific cell clusters.<dl>
 <dt>data</dt>
<dd>List of immune repertoire data frames.</dd> <dt>meta</dt>
<dd>Metadata</dd> ...</dl>

Format

Paired chain immune repertoire dataset — scdata

A list of four elements:
"data" is a list with data frames with clonotype tables.
"meta" is a metadata table.
"bc_patients" is a list of barcodes corresponding to specific patients.
"bc_clusters" is a list of barcodes corresponding to specific cell clusters.<dl>
 <dt>data</dt>
<dd>List of immune repertoire data frames.</dd>

 <dt>meta</dt>
<dd>Metadata</dd>

 ...

</dl>

Paired chain immune repertoire dataset

scdata: Paired chain immune repertoire dataset

Description

Usage

Arguments

Format