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CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments

H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens, Ryan M. O'Connell
2020 BMC Bioinformatics  
To improve the quality and efficiency of annotating cell clusters in scRNAseq data, we present a web-based R/Shiny app and R package, Cluster Identity PRedictor (CIPR), which provides a graphical user  ...  Single cell RNA sequencing (scRNAseq) has provided invaluable insights into cellular heterogeneity and functional states in health and disease.  ...  Consent to participate and consent for publication This is not applicable to this study as the CIPR pipeline was not developed with in-house human data.  ... 
doi:10.1186/s12859-020-3538-2 pmid:32414321 fatcat:e4m4ennacbh4rgp2crbec2pb5q

Automated methods for cell type annotation on scRNA-seq data

Giovanni Pasquini, Jesus Eduardo Rojo Arias, Patrick Schäfer, Volker Busskamp
2021 Computational and Structural Biotechnology Journal  
Cell type annotation is a crucial step in analyzing single-cell RNA sequencing data, yet manual annotation is time-consuming and partially subjective.  ...  The advent of single-cell sequencing started a new era of transcriptomic and genomic research, advancing our knowledge of the cellular heterogeneity and dynamics.  ...  Dresden and EXC-2151-390873048 -Cluster of Excellence -ImmunoSensation2 at the University of Bonn) and the Volkswagen Foundation (Freigeist -A110720).  ... 
doi:10.1016/j.csbj.2021.01.015 pmid:33613863 pmcid:PMC7873570 fatcat:bykhcbzy7rbdtg5fwg3k3ygzwm