Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang… - Nature …, 2024 - nature.com
With the advent of multiomics, software capable of multidimensional enrichment analysis
has become increasingly crucial for uncovering gene set variations in biological processes …

An overview of key online resources for human genomics: a powerful and open toolbox for in silico research

DA Forero, DA Bonilla… - Briefings in …, 2024 - academic.oup.com
Recent advances in high-throughput molecular methods have led to an extraordinary
volume of genomics data. Simultaneously, the progress in the computational implementation …

ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists

R Sethi, KS Ang, M Li, Y Long, J Ling, J Chen - Nature Communications, 2024 - nature.com
Abstract ezSingleCell is an interactive and easy-to-use application for analysing various
single-cell and spatial omics data types without requiring prior programing knowledge. It …

Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2. 0

A Jiang, L You, RG Snell… - NAR Genomics and …, 2023 - academic.oup.com
Complex biological traits and disease often involve patterns of gene expression that can be
characterised and examined. Here we present ICARUS v2. 0, an update to our single cell …

Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

N Mikolajewicz, R Gacesa, M Aguilera-Uribe… - Communications …, 2022 - nature.com
Single-cell RNA-sequencing (scRNA-seq) offers functional insight into complex biology,
allowing for the interrogation of cellular populations and gene expression programs at single …

ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells

A Jiang, RG Snell, K Lehnert - Bioinformatics, 2024 - academic.oup.com
Motivation In recent years, improvements in throughput of single cell RNA-seq have resulted
in a significant increase in the number of cells profiled. The generation of single cell RNA …

[HTML][HTML] Computational modeling for medical data: From data collection to knowledge discovery

Y Yang, S Xu, Y Hong, Y Cai, W Tang, J Wang… - The Innovation …, 2024 - the-innovation.org
Biomedical data encompasses images, texts, physiological signals, and molecular omics
data. As the costs of various data acquisition methods, such as genomic sequencing …

An AI Agent for Fully Automated Multi‐Omic Analyses

J Zhou, B Zhang, G Li, X Chen, H Li, X Xu… - Advanced …, 2024 - Wiley Online Library
With the fast‐growing and evolving omics data, the demand for streamlined and adaptable
tools to handle bioinformatics analysis continues to grow. In response to this need …

Ursa: A comprehensive multiomics toolbox for high-throughput single-cell analysis

L Pan, T Mou, Y Huang, W Hong… - Molecular Biology and …, 2023 - academic.oup.com
The burgeoning amount of single-cell data has been accompanied by revolutionary
changes to computational methods to map, quantify, and analyze the outputs of these cutting …

ShIVA: a user-friendly and interactive interface giving biologists control over their single-cell RNA-seq data

R Aussel, M Asif, S Chenag, S Jaeger, P Milpied… - Scientific Reports, 2023 - nature.com
Single-cell technologies have revolutionised biological research and applications. As they
continue to evolve with multi-omics and spatial resolution, analysing single-cell datasets is …