Milo is a method for differential abundance analysis on KNN graph from single-cell datasets. For more details, read our manuscript. If you use Milo in your study, please cite Dann, E., Henderson, N.C., Teichmann, S.A. et al. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nat Biotechnol (2021).
## Milo is available from Bioconductor (preferred stable installation) if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("miloR") ## Install development version devtools::install_github("MarioniLab/miloR", ref="devel")
milopyfor a full workflow in python)
An example of the
Milo work flow to get started:
data(sim_trajectory) milo.meta <- sim_trajectory$meta milo.obj <- Milo(sim_trajectory$SCE) milo.obj
Build a graph and neighbourhoods.
milo.obj <- buildGraph(milo.obj, k=20, d=30) milo.obj <- makeNhoods(milo.obj, k=20, d=30, refined=TRUE, prop=0.2)
Calculate distances, count cells according to an experimental design and perform DA testing.
milo.obj <- calcNhoodDistance(milo.obj, d=30) milo.obj <- countCells(milo.obj, samples="Sample", meta.data=milo.meta) milo.design <- as.data.frame(xtabs(~ Condition + Sample, data=milo.meta)) milo.design <- milo.design[milo.design$Freq > 0, ] rownames(milo.design) <- milo.design$Sample milo.design <- milo.design[colnames(nhoodCounts(milo.obj)),] milo.res <- testNhoods(milo.obj, design=~Condition, design.df=milo.design) head(milo.res)
For any question, feature request or bug report please create a new issue in this repository. If you have an error or code-based query, please provide
the executed code and the preceding code from the point of constructing the
Milo object, along with the output of your
sessionInfo() - this will help
us immeasurably to diagnose the issue.
We welcome contributions and suggestions from the community (though we may not take them onboard if they don't align with our development roadmap - please don't be offended). Please submit the initial idea as an issue, which we will discuss and ask for refinements/clarifications. If we approve the idea, then please open a pull request onto the devel branch, from which we will begin a review process. To smooth the process, please note that code changes must be backwards compatible, and must include all relevant unit tests.
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