Comparative Analysis of Packages and Algorithms for the Analysis of Spatially Resolved Transcriptomics Data

Natalie Charitakis, Mirana Ramialison, Hieu T. Nim

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

2 Citations (Scopus)


The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological tissues. The ability to interrogate how spatially localised gene expression can lend new insight to different tissue development is critical, but the appropriate tools to analyse this data are still emerging. This chapter reviews available packages and pipelines for the analysis of different SRT datasets with a focus on identifying spatially variable genes (SVGs) alongside other aims, while discussing the importance of and challenges in establishing a standardised ‘ground truth’ in the biological data for benchmarking.

Original languageEnglish
Title of host publicationTranscriptomics in Health and Disease
EditorsGeraldo A. Passos
Place of PublicationSwitzerland
Number of pages22
ISBN (Electronic)9783030878214
ISBN (Print)9783030878207
Publication statusPublished - 2022


  • Biological tissues
  • Gene regulatory networks
  • Organ development
  • Pipeline
  • ScRNA-Seq
  • Spatial biology
  • Spatial expression patterns
  • Spatial transcriptomics
  • SpatialDE
  • Spatially localised gene expression
  • Spatially resolved transcriptomics
  • Transcriptomic approaches

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