https://github.com/drisso/zinbwave

Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave
https://github.com/drisso/zinbwave

Last synced: 9 months ago
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Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave

• Host: GitHub
• URL: https://github.com/drisso/zinbwave
• Owner: drisso
• Created: 2017-08-30T22:00:06.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2024-03-13T20:20:22.000Z (about 2 years ago)
• Last Synced: 2024-12-17T13:51:37.855Z (over 1 year ago)
• Language: R
• Size: 649 KB
• Stars: 43
• Watchers: 7
• Forks: 10
• Open Issues: 10
• Metadata Files:
  • Readme: README.md

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README

          
# zinbwave

Zero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE)

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

[![BioC release](http://www.bioconductor.org/shields/build/release/bioc/zinbwave.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/zinbwave)

[![BioC devel](http://www.bioconductor.org/shields/build/release/bioc/zinbwave.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/zinbwave)

[![R-CMD-check](https://github.com/drisso/zinbwave/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/drisso/zinbwave/actions)

[![Coverage](https://codecov.io/gh/drisso/zinbwave/branch/master/graph/badge.svg)](https://codecov.io/gh/drisso/zinbwave)

This package implements a zero-inflated negative binomial model for single-cell RNA-seq data, with latent factors.

The model is described in details in the paper:

[D. Risso, F. Perraudeau, S. Gribkova, S. Dudoit and JP. Vert (2018).

A general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications.](https://www.nature.com/articles/s41467-017-02554-5)

## Installation

Since Bioconductor 3.7 the new recommended way to install Bioconductor packages is via the BiocManager package, available on CRAN:

```{r}

install.packages("BiocManager")

BiocManager::install("zinbwave")

```

Note that `zinbwave` requires `R (>=3.4)` and `Bioconductor (>=3.6)`.

In virtually all cases, installing from Bioconductor is recommended. However, if you want to install the development version of `zinbwave` from GitHub, you can do so with the following.

```{r}

library(devtools)

install_github("drisso/zinbwave")

```