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AbSim

Enables the simulation of time-resolved antibody repertoires. AbSim is an R package that allows user to comprehensively control the vast biologically-relevant parameter space of antibody repertoire selection and evolution. The control of the following parameters is possible by: (i) total time of evolution, (ii) rate and method of somatic hypermutation (SHM), (iii) number and rate of recombination events, (iv) rate at which new sequences are produced, (v) baseline mutation rate, (vi) clonal frequency, and (vii) germline gene usage distribution.

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AbSim versioning

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AbSim classification

AbSim specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
0.2.2
Requirements:
ape, poweRlaw
Source code URL:
https://cran.r-project.org/src/contrib/AbSim_0.2.2.tar.gz

AbSim support

Documentation

Maintainer

  • Alexander Yermanos <>

Credits

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Publications

Institution(s)

Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Institute of Microbiology, ETH Zürich, Zürich, Switzerland; Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland

Funding source(s)

Supported by SystemsX.ch AntibodyX RTD project, Swiss National Science Foundation (Project no: 31003A_143869, 31003A_170110), and Swiss Vaccine Research Institute.

Link to literature

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