https://github.com/pachterlab/voyager

From geospatial to spatial -omics
https://github.com/pachterlab/voyager

bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics

Last synced: 3 days ago
JSON representation

From geospatial to spatial -omics

• Host: GitHub
• URL: https://github.com/pachterlab/voyager
• Owner: pachterlab
• License: artistic-2.0
• Created: 2020-07-22T00:18:38.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2024-08-31T20:21:07.000Z (5 months ago)
• Last Synced: 2024-09-12T08:04:05.981Z (4 months ago)
• Topics: bioconductor, eda, esda, exploratory-data-analysis, omics, r, r-package, rstats, spatial, spatial-statistics, spatial-transcriptomics, transcriptomics
• Language: R
• Homepage: https://pachterlab.github.io/voyager/
• Size: 4.16 GB
• Stars: 70
• Watchers: 4
• Forks: 8
• Open Issues: 11
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING
  • License: LICENSE.md

Awesome Lists containing this project

README

        

# From geospatial to spatial transcriptomics

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

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

[![codecov](https://codecov.io/gh/pachterlab/voyager/branch/devel/graph/badge.svg?token=RCIXA7AQER)](https://codecov.io/gh/pachterlab/voyager)

This package brings the tradition of geospatial statistics to spatial omics by wrapping classical geospatial packages such as `spdep` and `gstat` to be used with the SpatialFeatureExperiment class, which extends SpatialExperiment with sf.

The [companion website](https://pachterlab.github.io/voyager/) for this package includes vignettes that showcase the functionality of `Voyager` in the context of the Visium, Slide-seq V2, CosMx, Xenium, and MERFISH technologies.  

## Installation

This package is in Bioconductor version 3.16 and above. Install with

```r

if (!requireNamespace("BiocManager")) install.packages("BiocManager")

BiocManager::install(version = "3.17") # Or a higher version in the future

BiocManager::install("Voyager")

```

The main branch in this repo is the release version. The development version of Voyager can be installed from [GitHub](https://github.com/) with:

```r

# install.packages("remotes")

remotes::install_github("pachterlab/voyager", ref = "devel")

```

Or from Bioconductor with:

```r

BiocManager::install("Voyager", version = "devel")

```

## For contributors

The whole git repo of this package is huge because of the large number of figures and Jupyter notebooks in the documentation website. To reduce download time and disk space usage, you may clone the `devel` branch only, so the documentation branches are not cloned:

```

git clone -b devel --single-branch https://github.com/pachterlab/voyager.git

```