miloR
This is thereleased version of miloR; for the devel version, seemiloR.
Differential neighbourhood abundance testing on a graph
Bioconductor version: Release (3.22)
Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either a negative bionomial generalized linear model or negative binomial generalized linear mixed model.
Author: Mike Morgan [aut, cre]
ORCID: 0000-0003-0757-0711, Emma Dann [aut, ctb]
Maintainer: Mike Morgan <michael.morgan at abdn.ac.uk>
citation("miloR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("miloR")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("miloR")| Differential abundance testing with Milo | HTML | R Script |
| Differential abundance testing with Milo - Mouse gastrulation example | HTML | R Script |
| Mixed effect models for Milo DA testing | HTML | R Script |
| Using contrasts for differential abundance testing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FunctionalGenomics,MultipleComparison,SingleCell,Software |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 years) |
| License | GPL-3 + fileLICENSE |
| Depends | R (>= 4.0.0),edgeR |
| Imports | BiocNeighbors,BiocGenerics,SingleCellExperiment,Matrix (>= 1.3-0),MatrixGenerics,S4Vectors, stats,stringr, methods,igraph,irlba, utils,cowplot,BiocParallel,BiocSingular,limma,ggplot2,tibble,matrixStats,ggraph,gtools,SummarizedExperiment,patchwork,tidyr,dplyr,ggrepel,ggbeeswarm,RColorBrewer, grDevices,Rcpp,pracma,numDeriv |
| System Requirements | |
| URL | https://marionilab.github.io/miloR |
| Bug Reports | https://github.com/MarioniLab/miloR/issues |
See More
| Suggests | testthat,mvtnorm,scater,scran,covr,knitr,rmarkdown,uwot,scuttle,BiocStyle,MouseGastrulationData,MouseThymusAgeing,magick,RCurl,MASS,curl,scRNAseq, graphics,sparseMatrixStats |
| Linking To | Rcpp,RcppArmadillo,RcppEigen,RcppML |
| Enhances | |
| Depends On Me | |
| Imports Me | dandelionR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | miloR_2.6.0.tar.gz |
| Windows Binary (x86_64) | miloR_2.6.0.zip (64-bit only) |
| macOS Binary (x86_64) | miloR_2.6.0.tgz |
| macOS Binary (arm64) | miloR_2.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/miloR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/miloR |
| Bioc Package Browser | https://code.bioconductor.org/browse/miloR/ |
| Package Short Url | https://bioconductor.org/packages/miloR/ |
| Package Downloads Report | Download Stats |