Biology subjects

Karlsen, V. T.

Publications and source records attributed to Karlsen, V. T..

2 recordsLinked to original sources

bioRxiv2023

cellsnake: a user-friendly tool for single cell RNA sequencing analysis

BackgroundSingle-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, non-expert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines. ResultsWe have developed cellsnake, a comprehensive, reproducible, and accessible single-cell data analysis workflow, to overcome these problems. Cellsnake offers advanced features for standard users and facilitates downstream analyses in both R and Python environments. It is also designed for easy integration into existing workflows, allowing for rapid analyses of multiple samples. ConclusionAs an open-source tool, cellsnake is accessible through Bioconda, PyPi, Docker, and GitHub, making it a cost-effective and user-friendly option for researchers. By using cellsnake, researchers can streamline the analysis of scRNA-seq data and gain insights into the complex biology of single cells.

bioinformatics↗

bioRxiv2021

Spatiotemporal single cell transcriptomic analyzis of human gut macrophages revealsmultiple functional and niche-specific subsets

Macrophages are a heterogeneous population of cells involved in tissue homeostasis, inflammation and cancer. Although macrophages are densely distributed throughout the human intestine, our understanding of how gut macrophages maintain tissue homeostasis is limited. Here we show that colonic lamina propria (LpM) and muscularis macrophages (MM) consist of monocyte-like cells that differentiate into multiple transcriptionally distinct subsets. LpM comprise subsets with proinflammatory properties and subsets high antigen presenting and phagocytic capacity. The latter are strategically positioned close to the surface epithelium. Most MM differentiate along two trajectories; one that upregulates genes associated with immune activation and angiogenesis, whereas the other upregulates genes associated with neuronal homeostasis. Importantly, MM are located adjacent to neurons and vessels. Cell-cell interaction and gene network analysis indicated that survival, migration, transcriptional reprogramming, and niche-specific localization of LpM and MM are controlled by an extensive interaction with tissue-resident cells and a few key transcription factors.

immunology↗