Search Results - Spatial Transcriptomics methods

Detection of differentially expressed genes in spatial transcriptomics data by spatial analysis of spatial transcriptomics: A novel method based on spatial statistics by Qiu, Zhihua, Li, Shaojun, Luo, Ming, Zhu, Shuanggen, Wang, Zhijian, Jiang, Yongjun

“…) based on the classical statistics, which should abolish the spatial information. A new method named spatial analysis of spatial transcriptomics (saSpatial…”
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Systematic comparison of sequencing-based spatial transcriptomic methods by You, Yue, Fu, Yuting, Li, Lanxiang, Zhang, Zhongmin, Jia, Shikai, Lu, Shihong, Ren, Wenle, Liu, Yifang, Xu, Yang, Liu, Xiaojing, Jiang, Fuqing, Peng, Guangdun, Sampath Kumar, Abhishek, Ritchie, Matthew E., Liu, Xiaodong, Tian, Luyi

“…Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed important advancements by facilitating transcriptome-scale spatial gene expression measurement…”
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Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data by Ouologuem, Sarah, Martens, Laura D, Schaar, Anna C, Shulman, Maiia, Gagneur, Julien, Theis, Fabian J

“… Spot deconvolution methods have been developed and extensively benchmarked for spatial transcriptomics, yet no dedicated methods exist for spatial chromatin accessibility, and it is unclear if RNA…”
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CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization by Georgaka, Sokratia, Morgans, William Geraint, Zhao, Qian, Martinez, Diego Sanchez, Ali, Amin, Ghafoor, Mohamed, Baker, Syed-Murtuza, Bristow, Robert G, Iqbal, Mudassar, Rattray, Magnus

“…Abstract Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity…”
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Benchmarking clustering, alignment, and integration methods for spatial transcriptomics by Hu, Yunfei, Xie, Manfei, Li, Yikang, Rao, Mingxing, Shen, Wenjun, Luo, Can, Qin, Haoran, Baek, Jihoon, Zhou, Xin Maizie

“…Background Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms…”
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Cell-type deconvolution methods for spatial transcriptomics by Gaspard-Boulinc, Lucie C, Gortana, Luca, Walter, Thomas, Barillot, Emmanuel, Cavalli, Florence M G

“…Spatial transcriptomics is a powerful method for studying the spatial organization of cells, which is a critical feature in the development, function and evolution of multicellular life…”
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Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods by Charitakis, Natalie, Salim, Agus, Piers, Adam T., Watt, Kevin I., Porrello, Enzo R., Elliott, David A., Ramialison, Mirana

“…Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data…”
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Evaluating spatially variable gene detection methods for spatial transcriptomics data by Chen, Carissa, Kim, Hani Jieun, Yang, Pengyi

“…Background The identification of genes that vary across spatial domains in tissues and cells is an essential step for spatial transcriptomics data analysis…”
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Integrative analysis methods for spatial transcriptomics by Lu, Shaina, Fürth, Daniel, Gillis, Jesse

“…Computational methods use different integrative strategies to tackle the challenges of spatially resolved transcriptomics data analysis…”
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Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data by Gingerich, Ian K., Goods, Brittany A., Frost, Hildreth Robert

“…Spatial transcriptomics (ST) provides critical insights into the spatial organization of gene expression, enabling researchers to unravel the intricate relationship between cellular environments and biological function…”
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Multiplexed spatial transcriptomics methods and the application of expansion microscopy by Fortner, Andra, Bucur, Octavian

“…While spatial transcriptomics has undeniably revolutionized our ability to study cellular organization, it has driven the development of a great number of innovative transcriptomics methods…”
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Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data? by Hafiz, Fahim, Azim, Riasat, Shatabda, Swakkhar

“…Abstract Recent advancements in spatially resolved transcriptomics (SRT) have enabled near single-cell resolution, providing rich spatial context crucial for uncovering biological insights…”
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Spatial transcriptomics iterative hierarchical clustering (stIHC): A novel method for identifying spatial gene co-expression modules by Higgins, Catherine, Li, Jingyi Jessica, Carey, Michelle

“… To address this, we present spatial transcriptomics iterative hierarchical clustering (stIHC), a novel method for clustering SVGs into co-expression modules, representing groups of genes with shared spatial expression patterns…”
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SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression by Liu, Yusong, Wang, Tongxin, Duggan, Ben, Sharpnack, Michael, Huang, Kun, Zhang, Jie, Ye, Xiufen, Johnson, Travis S

“…Abstract High-dimensional, localized ribonucleic acid (RNA) sequencing is now possible owing to recent developments in spatial transcriptomics (ST…”
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Current computational methods for spatial transcriptomics in cancer biology by Mo, Jaewoo, Bae, Junseong, Saqib, Jahanzeb, Hwang, Dohyun, Jin, Yunjung, Park, Beomsu, Park, Jeongbin, Kim, Junil

“… cellular behavior in the microenvironment. Spatial transcriptomics technology enables…”
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Benchmarking and integration of methods for deconvoluting spatial transcriptomic data by Yan, Lulu, Sun, Xiaoqiang

“…Abstract Motivation The rapid development of spatial transcriptomics (ST) approaches has provided new insights into understanding tissue architecture and function…”
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THItoGene: a deep learning method for predicting spatial transcriptomics from histological images by Jia, Yuran, Liu, Junliang, Chen, Li, Zhao, Tianyi, Wang, Yadong

“…Spatial transcriptomics unveils the complex dynamics of cell regulation and transcriptomes, but it is typically cost-prohibitive…”
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NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data by Chen, Yunlu, Ruan, Feng, Wang, Ji-Ping

“…Summary Spatial transcriptomics (ST) allows gene expression profiling within intact tissue samples but lacks single-cell resolution…”
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Development of a versatile LCM-Seq method for spatial transcriptomics of fluorescently tagged cholinergic neuron populations by Rumpler, Éva, Göcz, Balázs, Skrapits, Katalin, Sárvári, Miklós, Takács, Szabolcs, Farkas, Imre, Póliska, Szilárd, Papp, Márton, Solymosi, Norbert, Hrabovszky, Erik

“…Single-cell transcriptomics are powerful tools to define neuronal cell types based on co-expressed gene clusters…”
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Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding by Shen, Rongbo, Liu, Lin, Wu, Zihan, Zhang, Ying, Yuan, Zhiyuan, Guo, Junfu, Yang, Fan, Zhang, Chao, Chen, Bichao, Feng, Wanwan, Liu, Chao, Guo, Jing, Fan, Guozhen, Zhang, Yong, Li, Yuxiang, Xu, Xun, Yao, Jianhua

“… Here we propose Spatial-ID, a supervision-based cell typing method, that combines the existing knowledge of reference single-cell RNA-seq data and the spatial information of spatially resolved transcriptomics data…”
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