Completing spatial transcriptomics data for gene expression prediction benchmarking

Daniela Ruiz

doi:10.1016/j.media.2025.103754

2025-08-19

PRE

DOI：10.1016/j.media.2025.103754

原文链接

原文求助

摘要

En 中文

• 发布SpaRED，一个包含26个空间转录组学数据集的预处理数据集。 • 提出SpaCKLE，一种基于transformer的方法以完成缺失的基因表达。 • 对从组织学图像中获取基因表达数据的八种常见模型进行基准测试。 • 开源数据库和基因完成模型，附带易于使用的Python库。

Keyword:

SpaRED

SpaCKLE

spatial transcriptomics

gene expression completion

histology images

期刊

Medical Image Analysis

IF:

11.8

论文数:

3.8K

被引数:

2.4W

机构

暂无机构信息

引用论文

Integration tools for scRNA-seq data and spatial transcriptomics sequencing data 单细胞RNA测序数据与空间转录组学测序数据的整合工具

Briefings in Functional Genomics

IF0

2024-01-24

PREAI

Chaorui Yan; Yanxu Zhu; Miao Chen; Kainan Yang; Feifei Cui; Quan Zou; Zilong Zhang

ShuffleNet: An Extremely Efficient Convolutional Neural Network for Mobile Devices ShuffleNet: 一种用于移动设备的极其高效的卷积神经网络

2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition

IF0

2018-06-01

OAAI

Xiangyu Zhang; Xinyu Zhou; Mengxiao Lin; Jian Sun

Adjusting batch effects in microarray expression data using empirical Bayes methods 使用经验贝叶斯方法调整微阵列表达数据中的批次效应

Biostatistics

IF0

2006-04-21

OAAI

W. Evan Johnson; Cheng Li; Ariel Rabinovic

Comprehensive Integration of Single-Cell Data 单细胞数据的综合集成

Cell

IF0

2019-06-01

OAAI

Tim Stuart; Andrew Butler; Paul Hoffman; Christoph Hafemeister; Efthymia Papalexi; William M. Mauck; Yuhan Hao; Marlon Stoeckius; Peter Smibert; Rahul Satija

SEPAL: Spatial Gene Expression Prediction from Local Graphs

2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)

IF0

2023-10-02

OAAI

Gabriel Mejia; Paula Cárdenas; Daniela Ruiz; Angela Castillo; Pablo Arbeláez

Squidpy: a scalable framework for spatial omics analysis Squidpy: 一个可扩展的空间组学分析框架

NATURE METHODS

IF32.1

2022-01-31

293

OAAI

Palla, Giovanni; Spitzer, Hannah; Klein, Michal; Fischer, David; Schaar, Anna Christina; Kuemmerle, Louis Benedikt; Rybakov, Sergei; Ibarra, Ignacio L.; Holmberg, Olle; Virshup, Isaac; Lotfollahi, Mohammad; Richter, Sabrina; Theis, Fabian J.

Spatially resolved clonal copy number alterations in benign and malignant tissue 良性和恶性组织中空间分辨的克隆拷贝数改变

Nature

IF0

2022-08-10

OAAI

Andrew Erickson; Mengxiao He; Emelie Berglund; Maja Marklund; Reza Mirzazadeh; Niklas Schultz; Linda Kvastad; Alma Andersson; Ludvig Bergenstråhle; Joseph Bergenstråhle; Ludvig Larsson; Leire Alonso Galicia; Alia Shamikh; Elisa Basmaci; Teresita Díaz De Ståhl; Timothy Rajakumar; Dimitrios Doultsinos; Kim Thrane; Andrew L. Ji; Paul A. Khavari; Firaz Tarish; Anna Tanoglidi; Jonas Maaskola; Richard Colling; Tuomas Mirtti; Freddie C. Hamdy; Dan J. Woodcock; Thomas Helleday; Ian G. Mills; Alastair D. Lamb; Joakim Lundeberg

Robust mapping of spatiotemporal trajectories and cell-cell interactions in healthy and diseased tissues 健康和患病组织中时空轨迹和细胞-细胞相互作用的鲁棒映射

NATURE COMMUNICATIONS

IF15.7

2023-11-25

OAAI

Pham, Duy; Tan, Xiao; Balderson, Brad; Xu, Jun; Grice, Laura F.; Yoon, Sohye; Willis, Emily F.; Tran, Minh; Lam, Pui Yeng; Raghubar, Arti; Kalita-de Croft, Priyakshi; Lakhani, Sunil; Vukovic, Jana; Ruitenberg, Marc J.; Nguyen, Quan H.

Gene expression prediction from histology images via hypergraph neural networks 基于超图神经网络的组织学图像基因表达预测

BRIEFINGS IN BIOINFORMATICS

IF7.7

2024-10-14

OAAI

Li, Bo; Zhang, Yong; Wang, Qing; Zhang, Chengyang; Li, Mengran; Wang, Guangyu; Song, Qianqian

Spatially resolved, highly multiplexed RNA profiling in single cells 单细胞中空间分辨的、高度多重的RNA分析

Science

IF0

2015-04-24

OAAI

Kok Hao Chen; Alistair N. Boettiger; Jeffrey R. Moffitt; Siyuan Wang; Xiaowei Zhuang

查看更多内容