Ruth Seurinck

anndataR improves interoperability between R and Python in single-cell transcriptomics

anndataR enables interoperability between R and Python by allowing native reading and writing of H5AD files in R, with compatibility testing and conversion to R single-cell objects.

IL-1 instructs para-bronchial cuff fibroblasts to organize lung antibody secreting cell niches during continued antigen exposure

Continued allergen exposure drives lung TLO to generate ASCs that home to IL1-instructed para-bronchial cuffs.

SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis

SPArrOW is a pipeline for spatial transcriptomics analysis that improves data quality, provides visual quality checks, and enables interactive exploration and optimization of processing parameters.

Spotless: a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

The paper benchmarks 11 cell type deconvolution methods on spatial transcriptomics data using synthetic and real datasets, finding that some off-the-shelf methods outperform specialized ones.

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Combining pseudobulk differential expression, cell-type specificity, sample prevalence and NicheNet-v2 ligand activity, MultiNicheNet ranks condition-specific ligand-receptor-target signaling in multi-sample scRNA-seq with batches or multifactor designs.

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

This paper meta-analyzes single-cell method benchmarks to identify challenges in extensibility, interoperability, and reproducibility.

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

This study compares antibody- and lipid-based hashing methods for single-cell RNA-seq, finding antibody-based hashing more efficient and cost-effective for clinical samples.

Assessing robustness against potential publication bias in coordinate based fMRI meta-analyses using the Fail-Safe N

The paper develops a tool to assess robustness against publication bias in fMRI meta-analyses by simulating noise studies and testing parameter effects.

The Influence Of Study Characteristics On Coordinate-Based fMRI Meta-Analyses

This study evaluates how different factors affect the reliability and balance of false and true positives in coordinate-based fMRI meta-analyses.