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Alignment and integration of spatial transcriptomics data
Zeira, Ron, Land, Max, Strzalkowski, Alexander, Raphael, Benjamin J.
Published in Nature methods (01.05.2022)
Published in Nature methods (01.05.2022)
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Journal Article
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
DestVI identifies continuums of cell types in spatial transcriptomics data
Lopez, Romain, Li, Baoguo, Keren-Shaul, Hadas, Boyeau, Pierre, Kedmi, Merav, Pilzer, David, Jelinski, Adam, Yofe, Ido, David, Eyal, Wagner, Allon, Ergen, Can, Addadi, Yoseph, Golani, Ofra, Ronchese, Franca, Jordan, Michael I., Amit, Ido, Yosef, Nir
Published in Nature biotechnology (01.09.2022)
Published in Nature biotechnology (01.09.2022)
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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
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping
Clifton, Kalen, Anant, Manjari, Aihara, Gohta, Atta, Lyla, Aimiuwu, Osagie K., Kebschull, Justus M., Miller, Michael I., Tward, Daniel, Fan, Jean
Published in Nature communications (08.12.2023)
Published in Nature communications (08.12.2023)
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Journal Article
Estimation of cell lineages in tumors from spatial transcriptomics data
Ru, Beibei, Huang, Jinlin, Zhang, Yu, Aldape, Kenneth, Jiang, Peng
Published in Nature communications (02.02.2023)
Published in Nature communications (02.02.2023)
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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
SpotClean adjusts for spot swapping in spatial transcriptomics data
Ni, Zijian, Prasad, Aman, Chen, Shuyang, Halberg, Richard B., Arkin, Lisa M., Drolet, Beth A., Newton, Michael A., Kendziorski, Christina
Published in Nature communications (27.05.2022)
Published in Nature communications (27.05.2022)
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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
Cell clustering for spatial transcriptomics data with graph neural networks
Li, Jiachen, Chen, Siheng, Pan, Xiaoyong, Yuan, Ye, Shen, Hong-Bin
Published in Nature Computational Science (01.06.2022)
Published in Nature Computational Science (01.06.2022)
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Journal Article
Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST
Liu, Wei, Liao, Xu, Luo, Ziye, Yang, Yi, Lau, Mai Chan, Jiao, Yuling, Shi, Xingjie, Zhai, Weiwei, Ji, Hongkai, Yeong, Joe, Liu, Jin
Published in Nature communications (18.01.2023)
Published in Nature communications (18.01.2023)
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Journal Article
Library size confounds biology in spatial transcriptomics data
Bhuva, Dharmesh D., Tan, Chin Wee, Salim, Agus, Marceaux, Claire, Pickering, Marie A., Chen, Jinjin, Kharbanda, Malvika, Jin, Xinyi, Liu, Ning, Feher, Kristen, Putri, Givanna, Tilley, Wayne D., Hickey, Theresa E., Asselin-Labat, Marie-Liesse, Phipson, Belinda, Davis, Melissa J.
Published in Genome Biology (18.04.2024)
Published in Genome Biology (18.04.2024)
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Journal Article