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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

View ORCID ProfileBrenda Pardo, View ORCID ProfileAbby Spangler, View ORCID ProfileLukas M. Weber, View ORCID ProfileStephanie C. Hicks, View ORCID ProfileAndrew E. Jaffe, View ORCID ProfileKeri Martinowich, View ORCID ProfileKristen R. Maynard, View ORCID ProfileLeonardo Collado-Torres
doi: https://doi.org/10.1101/2021.04.29.440149
Brenda Pardo
1Licenciatura de Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, 76230, México;
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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Abby Spangler
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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Lukas M. Weber
3Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
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Stephanie C. Hicks
3Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
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Andrew E. Jaffe
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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Keri Martinowich
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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  • ORCID record for Keri Martinowich
Kristen R. Maynard
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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  • ORCID record for Kristen R. Maynard
Leonardo Collado-Torres
2Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
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  • ORCID record for Leonardo Collado-Torres
  • For correspondence: lcolladotor@gmail.com
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Abstract

Motivation Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissuespecific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary.

Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application.

Availability spatialLIBD is available at bioconductor.org/packages/spatialLIBD.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://research.libd.org/spatialLIBD/

  • https://bioconductor.org/packages/spatialLIBD

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted April 30, 2021.
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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado-Torres
bioRxiv 2021.04.29.440149; doi: https://doi.org/10.1101/2021.04.29.440149
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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado-Torres
bioRxiv 2021.04.29.440149; doi: https://doi.org/10.1101/2021.04.29.440149

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