Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bioconductor-source/spatialomicsoverlay

https://github.com/bioconductor-source/spatialomicsoverlay

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • License: mit
  • Language: R
  • Default Branch: devel
  • Size: 48.3 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

SpatialOmicsOverlay

Overview

The SpatialOmicsOverlay package contains tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP). It provides functions to extract image and XML from OME-TIFFs, overlay Regions of Interest (ROIs) onto the image, and manipulate the image (coloring, orientation, cropping). Output figures are ggplot based allowing for easy customization of images to include spatial images into data visualization.

Installation

Download the release version from Bioconductor

https://bioconductor.org/packages/release/bioc/html/SpatialOmicsOverlay.html

Install the release version from Bioconductor

``` r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager")

BiocManager::install(version="release")

BiocManager::install("SpatialOmicsOverlay") ```

Install the development version from GitHub

r install.packages("devtools") library("devtools") devtools::install_github("Nanostring-Biostats/SpatialOmicsOverlay", build_vignettes = TRUE, ref = "dev")

Documentation

To learn how to start using SpatialOmicsOverlay, view documentation for the version of this package installed in your system, start R and enter:

r browseVignettes("SpatialOmicsOverlay")

or download vignette from NanoString website (pending)

Branches

The dev branch on GitHub is under active development and no guarantee is made on usability at any given time. https://github.com/Nanostring-Biostats/SpatialOmicsOverlay

Citation

Griswold, M. SpatialOmicsOverlay: Spatial Overlay for Omic Data From Nanostring GeoMx data. R Package Version 0.99.10. NanoString Technologies Inc.; Seattle, WA 98109, USA. 2021.

License

This project is licensed under the MIT license.

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

GitHub Events

Total
Last Year

Dependencies

.github/workflows/main.yml actions
  • EddieHubCommunity/gh-action-community/src/welcome main composite
DESCRIPTION cran
  • R >= 4.1.0 depends
  • Biobase * imports
  • BiocFileCache * imports
  • EBImage * imports
  • GeomxTools * imports
  • RBioFormats * imports
  • S4Vectors * imports
  • XML * imports
  • base64enc * imports
  • data.table * imports
  • dplyr * imports
  • ggplot2 * imports
  • ggtext * imports
  • grDevices * imports
  • magick * imports
  • methods * imports
  • pbapply * imports
  • plotrix * imports
  • readxl * imports
  • scattermore * imports
  • stats * imports
  • stringr * imports
  • tools * imports
  • utils * imports
  • cowplot * suggests
  • knitr * suggests
  • pheatmap * suggests
  • qpdf * suggests
  • rmarkdown * suggests
  • sf * suggests
  • stringi * suggests
  • testthat >= 3.0.0 suggests
  • vdiffr * suggests
  • viridis * suggests