Ning Liu

hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data

hoodscanR identifies and analyzes cell neighborhoods in spatial transcriptomics data, revealing transcriptional differences in tumor cells across neighborhoods.

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

The paper examines DNA methylation dynamics in marsupial embryos, finding global demethylation in the trophectoderm but not the embryonic lineage, suggesting 5mC erasure in extraembryonic tissue is ancestral in therian mammals.

cellNexus: Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data

cellNexus enhances Human Cell Atlas data by adding quality control, metadata, normalization, and analysis layers to enable multi-study analyses and large-scale biological discovery.

Preserving tissue structure through density-based spatial analysis with scider

The paper introduces scider, a spatial analysis framework that preserves tissue structure by identifying regions of interest using kernel density estimation, enabling multi-sample analysis and revealing spatial patterns.

Decoding frontotemporal and cell type-specific vulnerabilities to neuropsychiatric disorders and psychoactive drugs

The paper identifies parvalbumin interneurons in the temporal lobe as highly vulnerable to genetic risk factors and psychoactive drugs in neuropsychiatric disorders.

Library size confounds biology in spatial transcriptomics data

This study shows that library size in spatial transcriptomics data confounds biological signals and recommends against normalizing it unless necessary.

vissE: A versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis

vissE identifies and visualizes higher-order molecular phenotypes from functional enrichment analysis by summarizing redundancies into biological themes.

standR: a Bioconductor package for analysing transcriptomic Nanostring GeoMx DSP data

standR is a Bioconductor package that improves the analysis of Nanostring GeoMx DSP spatial transcriptomic data by addressing technical variability and enhancing statistical power.

Seeing the forest through the trees: Identifying functional interactions from Hi-C

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk

This paper introduces 3DFAACTS-SNP, a workflow that identifies T1D risk variants with regulatory mechanisms using Treg-specific epigenomic data, finding 36 candidate SNPs and 51 target genes.