miloDE | Framework for sensitive DE testing

miloDE is a R library. miloDE has no bugs, it has no vulnerabilities and it has low support. However miloDE has a Non-SPDX License. You can download it from GitHub.

Framework for sensitive DE testing (using neighbourhoods). miloDE builds on an existing framework for DA testing called Milo. It exploits the notion of overlapping neighborhoods of homogeneous cells, constructed from graph-representation of scRNA-seq data, and performs testing within each neighborhood. Multiple testing correction is performed either across neighborhoods or across genes. Please see the preprint for greater details. In addition to DE testing, we provide functionality to rank neighbourhoods by degree of the DE as well as plotting functions to visualise results. In the vignette, we showcase how you can carry out clustering analysis to group genes in co-regulated transcriptional modules.