Giotto: a toolbox for integrative analysis and visualization of spatial expression data

被引：344
|
作者：
Dries, Ruben [1 ,2 ,3 ]
Zhu, Qian [1 ,2 ]
Dong, Rui [1 ,2 ]
Eng, Chee-Huat Linus [4 ]
Li, Huipeng [1 ,2 ]
Liu, Kan [5 ]
Fu, Yuntian [1 ,2 ]
Zhao, Tianxiao [1 ,2 ]
Sarkar, Arpan [1 ,2 ,6 ,7 ]
Bao, Feng [5 ]
George, Rani E. [1 ,2 ]
Pierson, Nico [4 ]
Cai, Long [4 ]
Yuan, Guo-Cheng [1 ,2 ,8 ,9 ]
机构：
[1] Dana Farber Canc Inst, Dept Pediat Oncol, Boston, MA 02115 USA
[2] Harvard Med Sch, Boston, MA 02115 USA
[3] Boston Univ, Sch Med, Boston, MA 02118 USA
[4] CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA
[5] Tsinghua Univ, Beijing, Peoples R China
[6] Harvard Univ, Dept Stat, Cambridge, MA 02138 USA
[7] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA
[8] Harvard Stem Cell Inst, Boston, MA USA
[9] Icahn Sch Med Mt Sinai, New York, NY 10029 USA
来源：
GENOME BIOLOGY | 2021年 / 22卷 / 01期
关键词：
GENE-EXPRESSION; CELL-TYPES; SINGLE; RECONSTRUCTION; IDENTIFICATION; TISSUE; SEQ;
D O I：
10.1186/s13059-021-02286-2
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
引用
收藏
页数：31
相关论文
共 50 条
  • [1] Giotto: a toolbox for integrative analysis and visualization of spatial expression data
    Ruben Dries
    Qian Zhu
    Rui Dong
    Chee-Huat Linus Eng
    Huipeng Li
    Kan Liu
    Yuntian Fu
    Tianxiao Zhao
    Arpan Sarkar
    Feng Bao
    Rani E. George
    Nico Pierson
    Long Cai
    Guo-Cheng Yuan
    [J]. Genome Biology, 22
  • [2] SmartHypnos: Developing a Toolbox for Polysomnographic Data Visualization and Analysis
    Chriskos, Panteleimon
    Frantzidis, Christos A.
    Gkivogkli, Polyxeni T.
    Papanastasiou, Emmanouil
    Kourtidou-Papadeli, Chrysoula
    Bamidis, Panagiotis D.
    [J]. 2019 41ST ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC), 2019, : 1395 - 1398
  • [3] Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration
    Wanichthanarak, Kwanjeera
    Fan, Sili
    Grapov, Dmitry
    Barupal, Dinesh Kumar
    Fiehn, Oliver
    [J]. PLOS ONE, 2017, 12 (01):
  • [4] MATLAB Toolbox for EnviSAT InSAR Data Processing, Visualization and Analysis
    Zhang, Zhidong
    Ma, Zunjing
    Chen, Ganlu
    Chen, Yan
    Lu, Yilong
    [J]. LAND SURFACE REMOTE SENSING, 2012, 8524
  • [5] RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
    Li, Zhijian
    Kuo, Chao-Chung
    Ticconi, Fabio
    Shaigan, Mina
    Gehrmann, Julia
    Gusmao, Eduardo Gade
    Allhoff, Manuel
    Manolov, Martin
    Zenke, Martin
    Costa, Ivan G.
    [J]. BMC BIOINFORMATICS, 2023, 24 (01)
  • [6] Analysis and Visualization of Spatial Transcriptomic Data
    Liu, Boxiang
    Li, Yanjun
    Zhang, Liang
    [J]. FRONTIERS IN GENETICS, 2022, 12
  • [7] RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data
    Zhijian Li
    Chao-Chung Kuo
    Fabio Ticconi
    Mina Shaigan
    Julia Gehrmann
    Eduardo Gade Gusmao
    Manuel Allhoff
    Martin Manolov
    Martin Zenke
    Ivan G. Costa
    [J]. BMC Bioinformatics, 24
  • [8] SEV - a software toolbox for large scale analysis and visualization of polysomnography data
    Moore, Hyatt E.
    Mignot, Emmanuel
    [J]. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION, 2015, 3 (03): : 123 - 135
  • [9] SOCRAT: A Dynamic Web Toolbox for Interactive Data Processing, Analysis and Visualization
    Kalinin, Alexandr A.
    Palanimalai, Selvam
    Zhu, Junqi
    Wu, Wenyi
    Devraj, Nikhil
    Ye, Chunchun
    Ponarul, Nellie
    Husain, Syed S.
    Dinov, Ivo D.
    [J]. INFORMATION, 2022, 13 (11)
  • [10] Spatial analysis and visualization of exploration geochemical data
    Zuo, Renguang
    Carranza, Emmanuel John M.
    Wang, Jian
    [J]. EARTH-SCIENCE REVIEWS, 2016, 158 : 9 - 18
12345