Details of the spatial transcriptomic analysis pipeline and R coding scripts can be found on our GitHub repository (https://github.com/wwq413/SpatialTranscriptomics)35. References Download references Acknowledgements We thank Hongyan Liu, Keke Yin, Man Jiang, Xue Song for bioinformatic assistance, samp...
Distinguishing cell types and subpopulations is a fundamental task in the bioinformatic analysis of spatial transcriptomics data. This can be resolved with the help of clustering analysis where spatially-variable genes can be discovered and data dimensions can be reduced through approaches such as princip...
文章在The Web-Based Portal SpatialTME Integrates Histological Images with Single-Cell and Spatial Transcriptomics to Explore the Tumor Microenvironment(cancer research ,IF 11.2)。 网址在SpatialTME,website link: http://www.spatialtme.yelab.site/ 肿瘤微环境(tumor microenvironment, TME)是一个复杂的...
nf-core/spatialvi is a bioinformatics analysis pipeline for Spatial Transcriptomics. It can process and analyse 10X spatial data either directly from raw data by running Space Ranger or data already processed by Space Ranger. The pipeline currently consists of the following steps: Raw data processing...
is applied to further reveal unified spatiotemporal changes and molecular fingerprints in the cartilage and synovium.70,71Initial research examining the synovium with the application of spatial transcriptomics focused on a comparative analysis between individuals diagnosed with rheumatoid arthritis (RA) and...
It covered the analysis of spatial transcriptomics data in Python, with tools like squidpy, node-centric expression models (ncem) as well as deconvolution (cell2location) and registration methods (eggplant). The workshop introduced the participants to both theoretical concepts as well as hands-on ...
This pipeline could be potentially generalized to most of the ST and SP approaches, thus advancing multi-omics cancer research and potentially clinical diagnostics in the future.Li Yen ChongInstitute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), ...
Most existing spatial transcriptome analysis methods are limited to single-slice spatial domain analysis, as they are unable to integrate gene expression and spatial information across multiple slices. However, with the advancement of spatial transcriptomics, it has become possible to obtain multiple slice...
Microfluidics-based single cell analysis: from transcriptomics to spatiotemporal multi-omics. Trac Trends Anal Chem. 2023;158:116868. CAS Google Scholar Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in ...
EASI-FISH Nextflow Pipeline This pipeline analyzes imagery collected using theEASI-FISH(Expansion-Assisted Iterative FluorescenceIn SituHybridization) method described inthis paper. It includes automated image stitching, distributed multi-round image registration, cell segmentation, and distributed spot detection...