Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics

被引：4

作者：

Pont, Frederic ^{[1
,2
,3
]}

Cerapio, Juan Pablo ^{[1
,2
,3
]}

Gravelle, Pauline ^{[1
,2
,3
]}

Ligat, Laetitia ^{[1
,2
,3
]}

Valle, Carine ^{[1
,2
,3
]}

Sarot, Emeline ^{[1
,2
,3
]}

Perrier, Marion ^{[1
,2
,3
]}

Lopez, Frederic ^{[1
,2
,3
]}

Laurent, Camille ^{[1
,2
,3
]}

Fournie, Jean Jacques ^{[1
,2
,3
]}

Tosolini, Marie ^{[1
,2
,3
]}

机构：

[1] Univ Toulouse III Paul Sabatier, Univ Toulouse, Ctr Rech Cancerol Toulouse, CRCT,CNRS,INSERM, Toulouse, France

[2] IUCT Oncopole, Toulouse, France

[3] TOUCAN, Lab Excellence Toulouse Canc, Toulouse, France

来源：

BMC BIOINFORMATICS | 2023年 / 24卷 / 01期

关键词：

Spatial transcriptomics; Single-cell; Multimodal analysis; Visualization; Open-source; Freeware; BOP GENE-CLUSTER; PROTEIN; PREDICTION; EXPRESSION; DIVERSITY;

D O I：

10.1186/s12859-023-05150-1

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background:The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called 'spatial transcriptomics'. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce.Results:Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies.Conclusions:Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.

引用

页数：12

共 50 条

[41] Combined Single-Cell and Spatial Transcriptomics to Deconvolute the Hematopoietic Stem Cell Niche
Haas, Simon
Baccin, Chiara
Al-Sabah, Jude
Velten, Lars
Lars, Steinmetz
Trumpp, Andreas
BLOOD, 2018, 132
[42] Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease
Piwecka, Monika
Rajewsky, Nikolaus
Rybak-Wolf, Agnieszka
NATURE REVIEWS NEUROLOGY, 2023, 19 (06) : 346 - 362
[43] Single-cell RNA sequencing and spatial transcriptomics of bladder Ewing sarcoma
Mao, Weipu
Xu, Kangjie
Wang, Keyi
Zhang, Houliang
Ji, Jie
Geng, Jiang
Sun, Si
Gu, Chaoming
Bhattacharya, Atrayee
Fang, Cheng
Tao, Tao
Chen, Ming
Wu, Jianping
Chen, Shuqiu
Sun, Chao
Xu, Bin
ISCIENCE, 2024, 27 (10)
[44] Single-cell and spatial transcriptomics: Discovery of human placental development and disease
Tang, Mi
Xiong, Liling
Cai, Jianghui
Fan, Li
Huang, Cheng
Zhang, Shimao
Jin, Ying
Luo, Er-dan
Xing, Shasha
Yang, Xiao
FASEB BIOADVANCES, 2024, 6 (11) : 503 - 518
[45] Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease
Monika Piwecka
Nikolaus Rajewsky
Agnieszka Rybak-Wolf
Nature Reviews Neurology, 2023, 19 : 346 - 362
[46] Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
Ratz, Michael
von Berlin, Leonie
Larsson, Ludvig
Martin, Marcel
Westholm, Jakub Orzechowski
La Manno, Gioele
Lundeberg, Joakim
Frisen, Jonas
NATURE NEUROSCIENCE, 2022, 25 (03) : 285 - +
[47] Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution
Tilburg, Julia
Stone, Andrew P.
Billingsley, James M.
Scoville, David K.
Pavenko, Anna
Liang, Yan
Italiano, Joseph E., Jr.
Machlus, Kellie R.
RESEARCH AND PRACTICE IN THROMBOSIS AND HAEMOSTASIS, 2023, 7 (04)
[48] Using advanced spatial and single-cell transcriptomics to characterize the human endometrium
Wang, Xiyin
Hawkins, Shannon M.
NATURE GENETICS, 2021, 53 (12) : 1628 - 1630
[49] Inferring single-cell and spatial microRNA activity from transcriptomics data
Herbst, Efrat
Mandel-Gutfreund, Yael
Yakhini, Zohar
Biran, Hadas
COMMUNICATIONS BIOLOGY, 2025, 8 (01)
[50] Using advanced spatial and single-cell transcriptomics to characterize the human endometrium
Xiyin Wang
Shannon M. Hawkins
Nature Genetics, 2021, 53 : 1628 - 1630

← 1 2 3 4 5 →