Givanna Putri

jazzPanda: spatially aware marker gene detection for imaging-based spatial transcriptomics

Binning transcript and cell coordinates into spatial vectors lets jazzPanda call smaller, spatially concordant marker sets than Wilcoxon or t-tests on Xenium/CosMx data, while modelling replicates and negative-control background.

Identifying the Minimal Number of Protein Markers for Cell Type Annotation Using MiniMarS

MiniMarS identifies the minimal number of protein markers for cell type annotation across multiple datasets and improves rare population identification.

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.

SuperCellCyto: enabling efficient analysis of large scale cytometry datasets

SuperCellCyto efficiently analyzes large cytometry datasets by grouping similar cells into supercells, avoiding the need for random subsampling.

Extraction and quantification of lineage-tracing barcodes with NextClone and CloneDetective

The paper introduces NextClone and CloneDetective for extracting and quantifying lineage-tracing barcodes from scRNA-seq and DNA sequencing data.

TrackSOM: mapping immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data

TrackSOM maps immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data, revealing heterogeneous immune cell populations and their functional evolution in West Nile Virus infection.