# miloR
_Milo_ is a method for differential abundance analysis on KNN graph from single-cell datasets. For more details, read [our manuscript](https://doi.org/10.1038/s41587-021-01033-z). 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)._
<p align="center">
<img src="docs/milo_schematic.png" width="500">
</p>
[![Build Status](https://travis-ci.com/MarioniLab/miloR.svg?branch=master)](https://travis-ci.com/MarioniLab/miloR)
[![Coverage](https://codecov.io/gh/MarioniLab/miloR/branch/master/graph/badge.svg)](https://codecov.io/gh/MarioniLab/miloR)
[![R-CMD-check](https://github.com/MarioniLab/miloR/actions/workflows/RCMD_check.yml/badge.svg)](https://github.com/MarioniLab/miloR/actions/workflows/RCMD_check.yml)
### Installation
```
## 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")
```
### Tutorials
1. [Basic Milo example on simulated dataset](https://bioconductor.org/packages/release/bioc/vignettes/miloR/inst/doc/milo_demo.html)
2. [Milo example on mouse gastrulation dataset](https://rawcdn.githack.com/MarioniLab/miloR/7c7f906b94a73e62e36e095ddb3e3567b414144e/vignettes/milo_gastrulation.html#5_Finding_markers_of_DA_populations): this includes a demo for downstream analysis functions.
3. [Integrating miloR in scanpy/anndata workflow](https://github.com/MarioniLab/milo_analysis_2020/blob/main/notebooks/milo_in_python.ipynb) (see also [`milopy`](https://github.com/emdann/milopy) for a full workflow in python)
4. [Specifying contrasts of interest for differential abundance testing with Milo](https://bioconductor.org/packages/release/bioc/vignettes/miloR/inst/doc/milo_contrasts.html)
### Example work flow
An example of the `Milo` work flow to get started:
```{r}
data(sim_trajectory)
milo.meta <- sim_trajectory$meta
milo.obj <- Milo(sim_trajectory$SCE)
milo.obj
```
Build a graph and neighbourhoods.
```{r}
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.
```{r}
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)
```
### Support
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.
### Contributions
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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Milo的R包实现,用于测试KNN图中的差异丰度_R_下.zip
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Milo的R包实现,用于测试KNN图中的差异丰度_R_下.zip (140个子文件)
docsearch.css 11KB
pkgdown.css 7KB
bootstrap-toc.css 2KB
DESCRIPTION 2KB
.gitignore 101B
.gitignore 4B
testDiffExp.html 48KB
milo_gastrulation.html 45KB
milo_demo.html 31KB
testNhoods.html 22KB
findNhoodMarkers.html 22KB
Milo.html 16KB
countCells.html 14KB
buildGraph.html 12KB
methods.html 11KB
makeNhoods.html 11KB
calcNhoodDistance.html 11KB
plotNhoodSizeHist.html 10KB
calcNhoodExpression.html 10KB
index.html 10KB
plotNhoodExpressionDA.html 9KB
buildFromAdjacency.html 9KB
graphSpatialFDR.html 8KB
index.html 8KB
annotateNhoods.html 8KB
plotDAbeeswarm.html 7KB
plotNhoodGraph.html 7KB
buildNhoodGraph.html 7KB
plotNhoodGraphDA.html 7KB
sim_trajectory.html 7KB
matrixORMatrix-class.html 6KB
sim_discrete.html 6KB
index.html 5KB
404.html 5KB
authors.html 5KB
bootstrap-toc.js 5KB
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LICENSE 34KB
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plotNhoods.R 33KB
findNhoodMarkers.R 15KB
test_graphSpatialFDR.R 15KB
test_testDiffExp.R 14KB
testDiffExp.R 13KB
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testNhoods.R 11KB
makeNhoods.R 10KB
test_findNhoodMarkers.R 10KB
findNhoodGroupMarkers.R 10KB
calcNhoodDistance.R 9KB
graphSpatialFDR.R 9KB
methods.R 9KB
test_makeNhoods.R 8KB
groupNhoods.R 8KB
test_findNhoodGroupMarkers.R 7KB
buildGraph.R 7KB
test_groupNhoodMarkers.R 7KB
test_calcNhoodDistance.R 7KB
milo.R 6KB
test_countCells.R 6KB
test_classes.R 6KB
test_annotateNhoods.R 6KB
test_calcNhoodExpression.R 5KB
test_buildFromAdjacency.R 5KB
test_buildGraph.R 5KB
countCells.R 4KB
buildFromAdjacency.R 4KB
calcNhoodExpression.R 3KB
test_buildNhoodGraph.R 3KB
annotateNhoods.R 3KB
AllClasses.R 3KB
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AllGenerics.R 2KB
buildNhoodGraph.R 2KB
sim_trajectory.R 695B
sim_discrete.R 679B
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