https://github.com/kieranrcampbell/mfa
Probabilistic inference of single-cell bifurcations
https://github.com/kieranrcampbell/mfa
bifurcation factor-analysis mixture-modelling single-cell
Last synced: 17 days ago
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Probabilistic inference of single-cell bifurcations
- Host: GitHub
- URL: https://github.com/kieranrcampbell/mfa
- Owner: kieranrcampbell
- Created: 2016-09-26T13:20:29.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2022-03-21T16:43:11.000Z (about 3 years ago)
- Last Synced: 2024-08-02T16:44:52.579Z (9 months ago)
- Topics: bifurcation, factor-analysis, mixture-modelling, single-cell
- Language: R
- Size: 77.1 KB
- Stars: 5
- Watchers: 6
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-single-cell - mfa - [R] - [Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers](https://wellcomeopenresearch.org/articles/2-19/v1) (Software packages / RNA-seq)
README
## mfa - Bayesian inference of bifurcations in single-cell data
`mfa` is an R package implementing Gibbs sampling for a Bayesian hierarchichal mixture of factor analysers for inference of bifurcations in single-cell data.
[](https://travis-ci.org/kieranrcampbell/mfa) [](https://doi.org/10.5281/zenodo.345981)
### Installation
`mfa` may be installed either via Bioconductor (coming soon) or Github:
#### Installation from Bioconductor
```r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("mfa")
```
#### Installation from Github
```r
devtools::install_github("kieranrcampbell/mfa", build_vignettes = TRUE)
```
### Usage
For a cell-by-gene matrix of expression Y, MFA can be envoked via
```r
m <- mfa(Y)
```
which will perform Gibbs sampling to infer pseudotimes, branch structure, and genes involved in the bifurcation.
For full usage see the package vignette:
```r
vignette('introduction_to_mfa')
```
### Authors
Kieran Campbell & Christopher Yau
University of Oxford