recipe bioconductor-sctreeviz

R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-sctreeviz/meta.yaml

scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.

package bioconductor-sctreeviz

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-epivizr >=2.28.0,<2.29.0

• bioconductor-epivizrdata >=1.26.0,<1.27.0

• bioconductor-epivizrserver >=1.26.0,<1.27.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-scater >=1.26.0,<1.27.0

• bioconductor-scran >=1.26.0,<1.27.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-clustree

• r-data.table

• r-digest

• r-ggplot2

• r-ggraph

• r-httr

• r-igraph

• r-matrix

• r-rtsne

• r-seurat

• r-sys

Required By:

Installation

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

conda install bioconductor-sctreeviz

and update with:

conda update bioconductor-sctreeviz

or use the docker container:

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

(see bioconductor-sctreeviz/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-sctreeviz/README.html)