Summary: This study introduces easySCF, a tool designed to enhance the interoperability of single-cell data between the two major bioinformatics platforms, R and Python. By supporting seamless data exchange, easySCF improves the efficiency and accuracy of single-cell data analysis.
Availability And Implementation: easySCF utilizes a unified data format (.h5 format) to facilitate data transfer between R and Python platforms. The tool has been evaluated for data processing speed, memory efficiency, and disk usage, as well as its capability to handle large-scale single-cell datasets. easySCF is available as an open-source package, with implementation details and documentation accessible at https://github.com/xleizi/easySCF.
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http://dx.doi.org/10.1093/bioinformatics/btae710 | DOI Listing |
Scand J Med Sci Sports
January 2025
Department of Surgical Sciences, Dentistry, Gynaecology and Paediatrics, University of Verona, Verona, Italy.
Previous studies in sports science suggested that regular exercise has a positive impact on human health. However, the effects of endurance sports and their underlying mechanisms are still not completely understood. One of the main debates regards the modulation of immune dynamics in high-intensity exercise.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
State Key Laboratory of Cellular Stress Biology, Xiang'an Hospital, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, No. 4221, Xiang'an South Road, Xiamen, Fujian 361102, China.
Enhancer clusters, pivotal in mammalian development and diseases, can organize as enhancer networks to control cell identity and disease genes; however, the underlying mechanism remains largely unexplored. Here, we introduce eNet 2.0, a comprehensive tool for enhancer networks analysis during development and diseases based on single-cell chromatin accessibility data.
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
The spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed to map the three-dimensional (3D) architecture of the genome, focusing on both ligation-based and ligation-free techniques. We also explore the limitations of these methods, including biases introduced by restriction enzyme digestion and ligation inefficiencies, and compare them to more recent ligation-free approaches such as Genome Architecture Mapping (GAM) and Split-Pool Recognition of Interactions by Tag Extension (SPRITE).
View Article and Find Full Text PDFTransl Cancer Res
December 2024
School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
Background: Regulatory T cells (Tregs) play a pivotal role in the development, prognosis, and treatment of breast cancer. This study aimed to develop a Treg-associated gene signature that contributes to predict prognosis and therapy benefits in breast cancer.
Methods: Treg-associated genes were screened based on single-cell RNA-sequencing (RNA-seq) in TISCH2 database and the bulk RNA-seq in The Cancer Genome Atlas (TCGA) database.
CNS Neurosci Ther
January 2025
Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
Background: Glioblastoma multiforme (GBM) is a common and highly aggressive brain tumor with a poor prognosis. However, the prognostic value of ferroptosis-related genes (FRGs) and their classification remains insufficiently studied.
Objective: This study aims to explore the significance of ferroptosis classification and its risk model in GBM using multi-omics approaches and to evaluate its potential in prognostic assessment.
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