Guangchuang Yu

Rho: A Purpose-Driven Workspace for Human-AI Collaborative Analysis

Rho is a collaborative analysis environment that organizes materials by scientific purpose to support human-AI judgment in bioinformatics.

ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity

ggalign provides a flexible R package for creating composable visualizations of complex, multi-dimensional biological data using layout options and annotation features.

EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research

EasyMultiProfiler provides a streamlined workflow for integrating and analyzing multi-omics microbiome data, addressing challenges in standardization and reproducibility.

Using fanyi to reduce language barriers, promote information absorption, and communication

The paper introduces the fanyi package, an AI-driven tool for translating and retrieving gene information to overcome language barriers in research.

Robust expansion of phylogeny for fast-growing genome sequence data

The paper introduces TIPars, an algorithm for efficiently expanding phylogenies with new genome sequences, showing it outperforms existing methods on multiple datasets.

Ggtree: a serialized data object for visualization of phylogenetic tree and annotation data

Ggtree creates a serialized data object for visualizing phylogenetic trees with associated annotations, enabling data reuse and reproducibility.

IOBR: Multi-omics Immuno-Oncology Biological Research to decode tumor microenvironment and signatures

IOBR is a computational tool that integrates multi-omics data to analyze tumor microenvironment and signatures, enabling batch analysis and comparison of immunotherapy-related features.

clusterProfiler: An universal enrichment tool for functional and comparative study

clusterProfiler performs over-representation (Fisher's exact test) and gene set enrichment analyses on Gene Ontology, KEGG, and user-supplied annotations, supporting non-model organisms, multi-condition comparisons, and ggplot2-based visualization.