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:

1.0.0-0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0a0

depends bioconductor-ggtreeextra:

>=1.12.0,<1.13.0a0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0a0

depends bioconductor-treeio:

>=1.26.0,<1.27.0a0

depends libgcc-ng:

>=12

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-domc:

depends r-doparallel:

depends r-dplyr:

depends r-foreach:

depends r-ggextra:

depends r-ggnewscale:

depends r-ggplot2:

depends r-gridextra:

depends r-igraph:

depends r-matrix:

depends r-matrixstats:

depends r-phangorn:

depends r-phytools:

depends r-pryr:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scavenge:

>=1.0.2,<1.1.0a0

depends r-seurat:

depends r-tibble:

depends r-tidytree:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-redeemr

and update with::

   mamba update r-redeemr

To create a new environment, run:

mamba create --name myenvname r-redeemr

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/r-redeemr:<tag>

(see `r-redeemr/tags`_ for valid values for ``<tag>``)

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