TY - JOUR
T1 - RCytoGPS
T2 - An R package for reading and visualizing cytogenetics data
AU - Abrams, Zachary B.
AU - Tally, Dwayne G.
AU - Abruzzo, Lynne V.
AU - Coombes, Kevin R.
N1 - Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected].
PY - 2021/12/1
Y1 - 2021/12/1
N2 - Summary: Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.
AB - Summary: Cytogenetics data, or karyotypes, are among the most common clinically used forms of genetic data. Karyotypes are stored as standardized text strings using the International System for Human Cytogenomic Nomenclature (ISCN). Historically, these data have not been used in large-scale computational analyses due to limitations in the ISCN text format and structure. Recently developed computational tools such as CytoGPS have enabled large-scale computational analyses of karyotypes. To further enable such analyses, we have now developed RCytoGPS, an R package that takes JSON files generated from CytoGPS.org and converts them into objects in R. This conversion facilitates the analysis and visualizations of karyotype data. In effect this tool streamlines the process of performing large-scale karyotype analyses, thus advancing the field of computational cytogenetic pathology.
UR - http://www.scopus.com/inward/record.url?scp=85122203478&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btab683
DO - 10.1093/bioinformatics/btab683
M3 - Article
C2 - 34601554
AN - SCOPUS:85122203478
SN - 1367-4803
VL - 37
SP - 4589
EP - 4590
JO - Bioinformatics
JF - Bioinformatics
IS - 23
ER -