recipe bioconductor-spiat

Spatial Image Analysis of Tissues

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/SPIAT.html

License:

Artistic-2.0

Recipe:

/bioconductor-spiat/meta.yaml

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

package bioconductor-spiat

Versions:

1.0.0-0

Depends:

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-dittoseq >=1.10.0,<1.11.0

• bioconductor-spatialexperiment >=1.8.0,<1.9.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-alphahull

• r-apcluster >=1.4.7

• r-base >=4.2,<4.3.0a0

• r-dbscan >=1.1-5

• r-dplyr >=0.8.3

• r-elsa

• r-ggplot2 >=3.2.1

• r-gridextra >=2.3

• r-gtools >=3.8.1

• r-mmand >=1.5.4

• r-plotly >=4.9.0

• r-pracma >=2.2.5

• r-rann >=2.6.1

• r-raster

• r-reshape2 >=1.4.3

• r-rlang

• r-rtsne

• r-sp

• r-spatstat.core

• r-spatstat.geom

• r-tibble >=2.1.3

• r-umap

• r-vroom

• r-xroi

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-spiat

and update with:

conda update bioconductor-spiat

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-spiat:<tag>

(see bioconductor-spiat/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-spiat/README.html)