Shixiang Wang

oxo-flow is a Rust-based workflow engine that compiles to a native binary, offering faster execution and lower memory usage compared to existing tools like Snakemake and Nextflow.

SigBridgeR benchmarks phenotype-associated cell subpopulations across four cancer types using eight algorithms, providing standardized workflows and visualization tools for reproducible analysis.

The paper introduces faers, an R/Bioconductor package that standardizes and automates FAERS data processing and signal detection for drug safety surveillance.

Onlinemeta provides a web-based tool for conducting meta-analysis and network meta-analysis with various analytical modules and visualizations.

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

This study integrates multi-omics data from NSCLC cohorts to identify molecular subtypes, revealing immune-activated and immunosuppressive subtypes with distinct prognostic implications.

ImmunoFusion integrates RNA-seq-derived gene fusion data across cancer types with tumor microenvironment and clinical outcomes to identify fusion-driven immunotherapy biomarkers.

IOBR2 is a tool for analyzing tumor microenvironment using multi-omics data, offering modules for preprocessing, estimation, interaction analysis, and visualization.

TCCIA integrates circRNA profiles, immunotherapy response data, and clinical outcomes to explore circRNA roles in cancer immunotherapy.

This study identifies 14 CNA signatures from pan-cancer WGS and TCGA SNP array data, revealing novel patterns and prognostic implications for cancer patients.

Hiplot provides a web service with 230+ interactive visualization tools for biomedical data, enabling users to generate publication-ready graphics without advanced expertise.

This study shows that Ggct deletion in mice causes splenomegaly and anemia due to oxidative damage and reduced glutathione in red blood cells.

This study identifies five copy number signatures in prostate cancer using sigminer, revealing distinct etiologies and improved clinical outcome associations compared to single base substitution signatures.

Sigflow is a pipeline for comprehensive cancer genome mutational signature analysis, supporting multiple DNA alteration types and offering reproducible research through Docker.

This paper critiques a previous study that claimed no neoantigen depletion signal in untreated cancer genomes, arguing that the study's methodology is flawed due to misalignment between defined HLA-binding regions and actual immunogenic neoantigens.