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STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization
Xu, Zhicheng, Wang, Weiwen, Yang, Tao, Li, Ling, Ma, Xizheng, Chen, Jing, Wang, Jieyu, Huang, Yan, Gould, Joshua, Lu, Huifang, Du, Wensi, Sahu, Sunil Kumar, Yang, Fan, Li, Zhiyong, Hu, Qingjiang, Hua, Cong, Hu, Shoujie, Liu, Yiqun, Cai, Jia, You, Lijin, Zhang, Yong, Li, YuXiang, Zeng, Wenjun, Chen, Ao, Wang, Bo, Liu, Longqi, Chen, Fengzhen, Ma, Kailong, Xu, Xun, Wei, Xiaofeng
Published in Nucleic acids research (05.01.2024)
Published in Nucleic acids research (05.01.2024)
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Journal Article
CellNeighborEX : deciphering neighbor‐dependent gene expression from spatial transcriptomics data
Kim, Hyobin, Kumar, Amit, Lövkvist, Cecilia, Palma, António M, Martin, Patrick, Kim, Junil, Bhoopathi, Praveen, Trevino, Jose, Fisher, Paul, Madan, Esha, Gogna, Rajan, Won, Kyoung Jae
Published in Molecular systems biology (09.11.2023)
Published in Molecular systems biology (09.11.2023)
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Journal Article
Points2Regions: Fast, interactive clustering of imaging‐based spatial transcriptomics data
Andersson, Axel, Behanova, Andrea, Avenel, Christophe, Windhager, Jonas, Malmberg, Filip, Wählby, Carolina
Published in Cytometry. Part A (01.09.2024)
Published in Cytometry. Part A (01.09.2024)
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Journal Article
Development of mutated β-catenin gene signature to identify CTNNB1 mutations from whole and spatial transcriptomic data in patients with HCC
Lehrich, Brandon M., Tao, Junyan, Liu, Silvia, Hirsch, Theo Z., Yasaka, Tyler M., Cao, Catherine, Delgado, Evan R., Guan, Xiangnan, Lu, Shan, Pan, Long, Liu, Yuqing, Singh, Sucha, Poddar, Minakshi, Bell, Aaron, Singhi, Aatur D., Zucman-Rossi, Jessica, Wang, Yulei, Monga, Satdarshan P.
Published in JHEP reports (01.12.2024)
Published in JHEP reports (01.12.2024)
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Journal Article
Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach
Zhang, Meng, Parker, Joel, An, Lingling, Liu, Yiwen, Sun, Xiaoxiao
Published in BMC bioinformatics (31.01.2025)
Published in BMC bioinformatics (31.01.2025)
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Journal Article
A count-based model for delineating cell–cell interactions in spatial transcriptomics data
Sarkar, Hirak, Chitra, Uthsav, Gold, Julian, Raphael, Benjamin J
Published in Bioinformatics (Oxford, England) (28.06.2024)
Published in Bioinformatics (Oxford, England) (28.06.2024)
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Journal Article
Spatial Transcriptomics of Human Postmortem Brain Tissue Uncovers Molecular Pathways Associated with Amyloid‐Beta Plaques
Avey, Denis, Ng, Bernard, Iatrou, Artemis, Vialle, Ricardo A, Lopes, Katia de Paiva, Tasaki, Shinya, Xu, Jishu, De Tissera, Sashini L, Flood, Daniel, Bennett, David A. A, Wang, Yanling
Published in Alzheimer's & dementia (01.12.2023)
Published in Alzheimer's & dementia (01.12.2023)
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Journal Article
Detection of differentially expressed genes in spatial transcriptomics data by spatial analysis of spatial transcriptomics: A novel method based on spatial statistics
Qiu, Zhihua, Li, Shaojun, Luo, Ming, Zhu, Shuanggen, Wang, Zhijian, Jiang, Yongjun
Published in Frontiers in neuroscience (29.11.2022)
Published in Frontiers in neuroscience (29.11.2022)
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Journal Article
Correction to ‘Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno’
Published in Nucleic acids research
(25.01.2024)
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Journal Article
LSGI: interpretable spatial gradient analysis for spatial transcriptomics data
Liang, Qingnan, Solis Soto, Luisa, Haymaker, Cara, Chen, Ken
Published in Genome Biology (08.08.2025)
Published in Genome Biology (08.08.2025)
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Journal Article
CPPLS-MLP: a method for constructing cell–cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data
Zhang, Tianjiao, Wu, Zhenao, Li, Liangyu, Ren, Jixiang, Zhang, Ziheng, Wang, Guohua
Published in Briefings in bioinformatics (27.03.2024)
Published in Briefings in bioinformatics (27.03.2024)
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Journal Article