Lambda Moses

This paper introduces concordex, a method to identify spatially homogeneous regions in tissues by decomposing gene expression patterns into cell-type and spatial variation, demonstrating its effectiveness across datasets.

This study compares Seurat and Scanpy, finding significant differences in their scRNA-seq analysis outputs, comparable to low sequencing depth or cell coverage.

Wayfarer analyzes spatial -omics data across multiple scales to reveal how spatial patterns change with resolution, showing shifts in tumor progression.

SpatialFeatureExperiment provides a Bioconductor package for handling spatial-omics data, integrating spatial analysis with single-cell omics workflows.

The paper describes using kallisto, bustools, and kb-python to quantify RNA-seq data from bulk, single-cell, and single-nucleus samples.

The paper introduces tidyomics, an ecosystem bridging Bioconductor and tidy R to streamline omic analysis using data from the Human Cell Atlas.

Geospatial exploratory statistics, including local, bivariate and multivariate spatial methods, are packaged for spatial omics behind one interface, with matched R/Bioconductor and Python implementations.

This study investigates the genetic basis of dietary iron overload and associated pathologies in mice using the Hybrid Mouse Diversity Panel, identifying genetic loci and pathways involved.

The paper curates a database of spatial transcriptomics literature and analyzes trends in experimental techniques, species, tissues, and computational methods.

The paper presents a modular and efficient workflow for single-cell RNA-seq pre-processing using kallisto and bustools, demonstrating its flexibility for RNA velocity analyses.