Integration of Computational Analysis and Spatial Transcriptomics in ...

Recent advances of single-cell transcriptomics technologies and allied computational methodologies have revolutionized molecular cell biology.

Semantic Scholar extracted view of "Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies" by Ran Wang et al.

A computational workflow for spatial transcriptomics

The workflow involves quality control, normalisation, data integration and cell type annotation using supervised labelling. Niche analysis was ...

Computational methods for alignment and integration of spatially ...

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016;353(6294):78–82. [PubMed] [Google ...

Advances in spatial transcriptomics and related data analysis ...

Additionally, CellTrek is a computational strategy that integrates scRNA-seq and spatial transcriptomics data sets to perform spatial ...

Integrating spatial and single-cell transcriptomics data using deep ...

We demonstrate SpatialScope's utility through simulation studies and real data analysis from both seq-based and image-based ST approaches.

Integration of Computational Analysis and Spatial Transcriptomics in ...

Here, we review the technical attributes of single-cell RNA sequencing and spatial transcriptomics, and the core concepts of computational data analysis. We ...

VisualZoneR: A computational protocol to identify compartmental ...

VisualZoneR is a computational approach developed in R for the integration and analysis of spatial transcriptomics data generated using Visium technology.

Integrating spatial transcriptomics data across different conditions ...

... spatially aware data integration, simultaneous spatial domain identification and downstream comparative analysis. We apply STAligner to ST ...

Computational solutions for spatial transcriptomics - ScienceDirect

The ST-framework Giotto (discussed in section 5.1.) uses enrichment-based options for cell type composition analysis [88] and Seurat anchor-based integration [ ...

Statistical and machine learning methods for spatially resolved ...

Theoretically, many of the computational approaches developed for scRNA-seq data analysis could be adapted to study spatial transcriptomics data ...

Benchmarking Computational Integration Methods for Spatial ...

Since SV genes are often used as features in downstream spatial transcriptomics data analysis, we used the results obtained from using SV genes as the ...

Computational Approaches and Challenges in Spatial Transcriptomics

Spatial transcriptomics, Computational approach, Data ... J. Seamless integration of image and molecular analysis for spatial transcriptomics workflows.

Benchmarking and integration of methods for deconvoluting spatial ...

L. et al. (. 2016. ) Visualization and analysis of gene expression in tissue sections by spatial transcriptomics . Science. ,. 353. ,. 78. –. 82.

Publication Highlight: Benchmarking Methods to Integrate Spatial ...

In the paper Benchmarking spatial and single-cell transcriptomics integration ... Computational resource consumption. Specific areas each ...

Updated computational tools for spatial transcriptomics analysis

The second task it can perform is multi-sample integration to overcome batch effects in spatial data between sections by jointly projecting data ...

Integrating Single Cell and Visium Spatial Gene Expression Data

The current computational tools for single cell and Visium integration fall on a continuum between deconvolution and mapping approaches. Deconvolution methods ...

A guidebook of spatial transcriptomic technologies, data resources ...

Moreover, novel computational tools for integrating spatial transcriptomics ... Seamless integration of image and molecular analysis for spatial transcriptomics ...

A computational pipeline for spatial mechano-transcriptomics

... spatial analysis at the subcellular scale and is a member of the open-source Scverse ecosystem, enabling integration with other single-cell omics analysis tools ...

Benchmarking Computational Integration Methods for Spatial ...

... analysis methods for various ST technologies [97] . ... Emerging Artificial Intelligence Applications in Spatial Transcriptomics Analysis.