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SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data
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AbstractSummarySCAPE is a package we previously developed to estimate alternative polyadenylation events from single cell RNA-seq (scRNA-seq) data, which is composed of ad-hoc python scripts and has speed issues when handling large scRNA-seq data. To suit the needs of analyzing large scRNA-seq datasets, we present SCAPE-APA, which is a re-implementation of SCAPE with substantial changes. We made the following updates to the package (1) we binned similar reads together to accelerate the estimation (2) we re-derived the mixture model to tailor it for binned reads (3) we implemented the inference algorithm using Taichi language for acceleration (4) we re-implemented the untranslated region (UTR) annotation extraction script using the professional package gffutils for better maintenance (5) we wrote a script to detect spurious alternative polyadenylation sites generated due to junction reads and (6) we made a formal python package and uploaded it to the Python Package Index website (Pypi).Availability and ImplementationScape-apa is freely available athttps://github.com/chengl7-lab/scapeand can be easily installed using pip.Contactlu.cheng.ac@gmail.com
Title: SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data
Description:
AbstractSummarySCAPE is a package we previously developed to estimate alternative polyadenylation events from single cell RNA-seq (scRNA-seq) data, which is composed of ad-hoc python scripts and has speed issues when handling large scRNA-seq data.
To suit the needs of analyzing large scRNA-seq datasets, we present SCAPE-APA, which is a re-implementation of SCAPE with substantial changes.
We made the following updates to the package (1) we binned similar reads together to accelerate the estimation (2) we re-derived the mixture model to tailor it for binned reads (3) we implemented the inference algorithm using Taichi language for acceleration (4) we re-implemented the untranslated region (UTR) annotation extraction script using the professional package gffutils for better maintenance (5) we wrote a script to detect spurious alternative polyadenylation sites generated due to junction reads and (6) we made a formal python package and uploaded it to the Python Package Index website (Pypi).
Availability and ImplementationScape-apa is freely available athttps://github.
com/chengl7-lab/scapeand can be easily installed using pip.
Contactlu.
cheng.
ac@gmail.
com.
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