PT  - JOURNAL ARTICLE
AU  - Aksman, Leon M.
AU  - Wijeratne, Peter A.
AU  - Oxtoby, Neil P.
AU  - Eshaghi, Arman
AU  - Shand, Cameron
AU  - Altmann, Andre
AU  - Alexander, Daniel C.
AU  - Young, Alexandra L.
TI  - pySuStaIn: a Python implementation of the Subtype and Stage Inference algorithm
AID  - 10.1101/2021.06.09.447713
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.06.09.447713
4099  - http://biorxiv.org/content/early/2021/06/10/2021.06.09.447713.short
4100  - http://biorxiv.org/content/early/2021/06/10/2021.06.09.447713.full
AB  - Progressive disorders are highly heterogeneous. Symptom-based clinical classification of these disorders may not reflect the underlying pathobiology. Data-driven subtyping and staging of patients has the potential to disentangle the complex spatiotemporal patterns of disease progression. Tools that enable this are in high demand from clinical and treatment-development communities. Here we describe the pySuStaIn software package, a Python-based implementation of the Subtype and Stage Inference (SuStaIn) algorithm. SuStaIn unravels the complexity of heterogeneous diseases by inferring multiple disease progression patterns (subtypes) and individual severity (stages) from cross-sectional data. The primary aims of pySuStaIn are to enable widespread application and translation of SuStaIn via an accessible Python package that supports simple extension and generalization to novel modelling situations within a single, consistent architecture.Code metadata Current code version v1.0Permanent link to code/repository used of this code version https://github.com/ucl-pond/pySuStaInLegal Code License MITCode versioning system used gitSoftware code languages, tools, and services used PythonCompilation requirements, operating environments & dependencies Linux, Mac, WindowsSupport email for questions leon.aksman{at}loni.usc.edu, p.wijeratne{at}ucl.ac.uk, alexandra.young{at}kcl.ac.ukCompeting Interest StatementThe authors have declared no competing interest.