Package Recipe 'r-redeemr'

recipe r-redeemr

R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling.

Homepage:: https://github.com/chenweng1991/redeemR
Documentation:: https://chenweng1991.github.io/redeemR
License:: MIT / MIT
Recipe:: /r-redeemr/meta.yaml

Introduce a new approach for single-cell Regulatory multi-omics (transcriptomics and chromatin accessibility) with Deep Mitochondrial mutation profiling (~10-fold increase in detection rate), or ReDeeM. redeemR is the R package that facilitates mutation refining, lineage tracing, as well multiomics integration analysis.

package r-redeemr¶

Versions:

1.0.0-1, 1.0.0-0

Depends:

on bioconductor-ggtree >=3.14.0,<3.15.0a0
on bioconductor-ggtreeextra >=1.16.0,<1.17.0a0
on bioconductor-qvalue >=2.38.0,<2.39.0a0
on bioconductor-treeio >=1.30.0,<1.31.0a0
on libgcc >=13
on r-ape
on r-base >=4.4,<4.5.0a0
on r-domc
on r-doparallel
on r-dplyr
on r-foreach
on r-ggextra
on r-ggnewscale
on r-ggplot2
on r-gridextra
on r-igraph
on r-matrix
on r-matrixstats
on r-phangorn
on r-phytools
on r-pryr
on r-rcolorbrewer
on r-reshape2
on r-scavenge >=1.0.2,<1.1.0a0
on r-seurat
on r-tibble
on r-tidytree

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 r-redeemr

to add into an existing workspace instead, run:

pixi add r-redeemr

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-redeemr

Alternatively, to install into a new environment, run:

conda create -n envname r-redeemr

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-redeemr:<tag>

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