Package Recipe 'bioconductor-hgc'

recipe bioconductor-hgc

A fast hierarchical graph-based clustering method

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/HGC.html
License:: GPL-3
Recipe:: /bioconductor-hgc/meta.yaml

HGC (short for Hierarchical Graph-based Clustering) is an R package for conducting hierarchical clustering on large-scale single-cell RNA-seq (scRNA-seq) data. The key idea is to construct a dendrogram of cells on their shared nearest neighbor (SNN) graph. HGC provides functions for building graphs and for conducting hierarchical clustering on the graph. The users with old R version could visit https://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get HGC package built for R 3.6.

package bioconductor-hgc¶

Versions:

1.18.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-2, 1.6.0-1, 1.6.0-0, 1.2.0-2, 1.2.0-1,

1.18.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-2, 1.6.0-1, 1.6.0-0, 1.2.0-2, 1.2.0-1, 1.2.0-0, 1.0.0-0

Depends:

on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-dendextend
on r-dplyr
on r-ggplot2
on r-matrix
on r-mclust
on r-patchwork
on r-rann
on r-rcpp >=1.0.0
on r-rcppeigen >=0.3.2.0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-hgc

to add into an existing workspace instead, run:

pixi add bioconductor-hgc

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-hgc

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-hgc

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-hgc/README.html)