Dharmesh D. Bhuva

Abstract Pancreatic ductal adenocarcinoma (PDAC) is driven by genetic alterations in the pancreatic epithelium (e.g., KRAS) coupled with dysregulated innate immunity that triggers tumor-promoting chronic inflammation. However, the identity of innate immune molecular regulators as therapeutic targets in PDAC is ill-defined.

Abstract Library size normalisation is necessary to enable comparisons between observations in transcriptomic datasets. Numerous methods have been developed to normalise these effects with sample and gene specific adjustments. However, in spatial transcriptomics data, normalisation is complicated by the fact that spatial region-specific library size confounds biology.

Abstract Understanding complex cellular niches and neighborhoods are giving us new insights into tissue biology. Accurate neighborhood identification is crucial, yet existing methodologies often struggle to detect mixed neighborhoods and generate cell-specific neighborhood profiles. To address these limitations, we introduce hoodscanR, a Bioconductor package designed for neighborhood identification and downstream analyses using spatial data.