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Overview

By design, immundata splits the analysis workflow into two clear phases:

  1. Ingestion – convert your AIRR files into a special format saved on disk, and then read them to a tidy ImmunData object.

  2. Transformation – explore, annotate, filter and compute on that object.

Before we go into more details for each of the phase, there are three straightforward yet essential concepts to keep in mind:

  1. Data units.

  2. Aggregation of receptors and repertoires.

  3. Pipeline-based execution.

These concepts set it apart from data-frame-based AIRR libraries. By extension, the concepts affect how you would work with and even think about the data analysis in other packages such as immunarch which use immundata as a backbone for computations.