SpatialDE: identification of spatially variable genes

Svensson, Valentine, Teichmann, Sarah A, Stegle, Oliver·2018·Nature Methods
DOI 10.1038/nmeth.4636

Cited by (710)

Items 601–700 of 710

  1. Additional file 13 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  2. Additional file 14 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  3. Additional file 1 of Automated identification of the mouse brain’s spatial compartments from in situ sequencing data
    Partel, Gabriele, Markus M. Hilscher, Giorgia Milli, Leslie Solorzano, Klemm, Anna H., Nilsson, Mats, Carolina Wählby · 2021 · Figshare
  4. Additional file 2 of BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies
    Li, Zheng, Zhou, Xiang · 2022 · Figshare
  5. Additional file 12 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  6. Additional file 3 of spVC for the detection and interpretation of spatial gene expression variation
    Shan Yu, Wei Vivian Li · 2024 · Figshare
  7. Additional file 2 of Evaluating spatially variable gene detection methods for spatial transcriptomics data
    Carissa Chen, Kim, Hani Jieun, Pengyi Yang · 2024 · Figshare
  8. Additional file 1 of SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
    Zhu, Jiaqiang, Lulu Shang, Zhou, Xiang · 2024 · Figshare
  9. Additional file 1 of BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies
    Li, Zheng, Zhou, Xiang · 2022 · Figshare
  10. Additional file 6 of SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
    Zhu, Jiaqiang, Sun, Shiquan, Zhou, Xiang · 2021 · Figshare
  11. Additional file 1 of Explainable multiview framework for dissecting spatial relationships from highly multiplexed data
    Jovan Tanevski, Flores, Ricardo Omar Ramirez, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez · 2022 · Figshare
  12. Additional file 3 of MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data
    Wang, Yu, Liu, Zaiyi, Ma, Xiaoke · 2024 · Figshare
  13. Additional file 3 of Giotto: a toolbox for integrative analysis and visualization of spatial expression data
    Ruben Dries, Zhu, Qian, Dong, Rui, Eng, Chee-Huat Linus, Li, Huipeng, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Bao, Feng et al. · 2021 · Figshare
  14. Additional file 1 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  15. Additional file 9 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  16. Additional file 8 of Modeling zero inflation is not necessary for spatial transcriptomics
    Peiyao Zhao, Zhu, Jiaqiang, Ma, Ying, Zhou, Xiang · 2022 · Figshare
  17. Additional file 1 of Giotto: a toolbox for integrative analysis and visualization of spatial expression data
    Ruben Dries, Zhu, Qian, Dong, Rui, Eng, Chee-Huat Linus, Li, Huipeng, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Bao, Feng et al. · 2021 · Figshare
  18. Additional file 1 of Spatial omics technologies at multimodal and single cell/subcellular level
    Jiwoon Park, Junbum Kim, Tyler Lewy, Rice, Charles M., Elemento, Olivier, Rendeiro, André F., Mason, Christopher E. · 2023 · Figshare
  19. Additional file 7 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  20. Additional file 1 of SRT-Server: powering the analysis of spatial transcriptomic data
    Yang, Sheng, Zhou, Xiang · 2024 · Figshare
  21. Additional file 15 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  22. Additional file 2 of Giotto: a toolbox for integrative analysis and visualization of spatial expression data
    Ruben Dries, Zhu, Qian, Dong, Rui, Eng, Chee-Huat Linus, Li, Huipeng, Liu, Kan, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Bao, Feng et al. · 2021 · Figshare
  23. Additional file 7 of Modeling zero inflation is not necessary for spatial transcriptomics
    Peiyao Zhao, Zhu, Jiaqiang, Ma, Ying, Zhou, Xiang · 2022 · Figshare
  24. Additional file 2 of Seamless integration of image and molecular analysis for spatial transcriptomics workflows
    Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg · 2020 · Figshare
  25. Additional file 4 of SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
    Zhu, Jiaqiang, Lulu Shang, Zhou, Xiang · 2024 · Figshare
  26. Additional file 18 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  27. Additional file 4 of MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data
    Wang, Yu, Liu, Zaiyi, Xiaoke Ma · 2024 · Figshare
  28. Additional file 2 of spVC for the detection and interpretation of spatial gene expression variation
    Shan Yu, Wei Vivian Li · 2024 · Figshare
  29. Additional file 4 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  30. Additional file 1 of Evaluating spatially variable gene detection methods for spatial transcriptomics data
    Carissa Chen, Kim, Hani Jieun, Pengyi Yang · 2024 · Figshare
  31. Additional file 5 of Giotto: a toolbox for integrative analysis and visualization of spatial expression data
    Ruben Dries, Zhu, Qian, Dong, Rui, Eng, Chee-Huat Linus, Li, Huipeng, Liu, Kan, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Bao, Feng et al. · 2021 · Figshare
  32. Additional file 2 of MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data
    Wang, Yu, Liu, Zaiyi, Ma, Xiaoke · 2024 · Figshare
  33. Additional file 3 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  34. Additional file 2 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, Rachel Patton McCord · 2021 · Figshare
  35. Additional file 1 of MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data
    Wang, Yu, Liu, Zaiyi, Ma, Xiaoke · 2024 · Figshare
  36. Additional file 2 of Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
    Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Stephanie C. Page, Stephanie C. Hicks, Maynard, Kristen R., Leonardo Collado‐Torres · 2024 · Figshare
  37. Additional file 8 of CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
    Xu, Yang, McCord, Rachel Patton · 2021 · Figshare
  38. Additional file 1 of Seamless integration of image and molecular analysis for spatial transcriptomics workflows
    Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg · 2020 · Figshare
  39. Additional file 1 of spVC for the detection and interpretation of spatial gene expression variation
    Shan Yu, Wei Vivian Li · 2024 · Figshare
  40. Additional file 2 of Explainable multiview framework for dissecting spatial relationships from highly multiplexed data
    Jovan Tanevski, Flores, Ricardo Omar Ramirez, Attila Gábor, Denis Schapiro, Julio Sáez-Rodríguez · 2022 · Figshare
  41. Additional file 2 of SRT-Server: powering the analysis of spatial transcriptomic data
    Yang, Sheng, Zhou, Xiang · 2024 · Figshare
  42. Additional file 3 of SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
    Zhu, Jiaqiang, Lulu Shang, Zhou, Xiang · 2024 · Figshare
  43. Additional file 5 of SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics
    Zhu, Jiaqiang, Lulu Shang, Zhou, Xiang · 2024 · Figshare
  44. Deconvolution-Enhanced Contrastive Pretraining of Histology Images and Gene Expressions in Spatial Transcriptomics
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    Aoqi Xie, Yuehua Cui · 2026 · Advanced Intelligent Systems
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  49. Mitigating bias in spatial transcriptomic pipelines via human feedback with CSDE
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  51. SpaMCI-DL: A Hybrid Deep Learning Framework for Integrated Identification of Domains and Spatially Variable Genes in Spatial Transcriptomics
    Xiao Liang, Pei Liu, Cong Shen, Wei Liu, Juping Li, Jiawei Luo · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  52. An Integrated Pipeline for Cell-Type Annotation, Metabolic Profiling, and Spatial Communication Analysis in the Liver using Spatial Transcriptomics
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