Package Recipe 'r-archr'

recipe r-archr

This package is designed to streamline scATAC analyses in R.

Homepage:: https://www.archrproject.com
Documentation:: https://www.archrproject.com/bookdown/index.html
Developer docs:: https://github.com/GreenleafLab/ArchR
License:: MIT / MIT
Recipe:: /r-archr/meta.yaml
Links:: doi: 10.1038/s41588-021-00790-6, biotools: archr

package r-archr¶

Versions:

1.0.3-4, 1.0.3-3, 1.0.3-2, 1.0.3-0, 1.0.2-0

Depends:

on bioconductor-biocgenerics >=0.52.0,<0.53.0a0
on bioconductor-biostrings >=2.74.0,<2.75.0a0
on bioconductor-chromvar >=1.30.1,<2.0a0
on bioconductor-complexheatmap >=2.22.0,<2.23.0a0
on bioconductor-genomicranges >=1.58.0,<1.59.0a0
on bioconductor-motifmatchr >=1.28.0,<1.29.0a0
on bioconductor-rhdf5 >=2.50.0,<2.51.0a0
on bioconductor-rsamtools >=2.22.0,<2.23.0a0
on bioconductor-s4vectors >=0.44.0,<0.45.0a0
on bioconductor-s4vectors >=0.9.25
on bioconductor-sparsematrixstats >=1.18.0,<1.19.0a0
on bioconductor-summarizedexperiment >=1.36.0,<1.37.0a0
on libgcc >=13
on libstdcxx >=13
on r-base >=4.4,<4.5.0a0
on r-chromvarmotifs >=0.2.0,<0.3.0a0
on r-data.table
on r-devtools
on r-ggplot2
on r-ggrastr
on r-ggrepel
on r-gridextra
on r-gtable
on r-gtools
on r-harmony
on r-magrittr
on r-matrix
on r-matrixstats
on r-nabor
on r-plyr
on r-presto >=1.0.0,<2.0a0
on r-rcpp >=0.12.16
on r-rcpparmadillo
on r-seurat
on r-seuratobject
on r-stringr
on r-uwot

Additional platforms:

linux-aarch64, osx-arm64

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 r-archr

to add into an existing workspace instead, run:

pixi add r-archr

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 r-archr

Alternatively, to install into a new environment, run:

conda create -n envname r-archr

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/r-archr:<tag>

(see r-archr/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/r-archr/README.html)