recipe r-numbat

A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.

Homepage:

https://github.com/kharchenkolab/numbat/, https://kharchenkolab.github.io/numbat/

License:

MIT / MIT

Recipe:

/r-numbat/meta.yaml

package r-numbat

versions:

1.4.2-0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0a0

depends bioconductor-ggtree:

>=3.14.0,<3.15.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends r-ape:

depends r-base:

>=4.4,<4.5.0a0

depends r-catools:

depends r-data.table:

depends r-dendextend:

depends r-dplyr:

>=1.1.1

depends r-ggplot2:

depends r-ggraph:

depends r-glue:

depends r-hahmmr:

>=1.0.0,<1.1.0a0

depends r-igraph:

depends r-logger:

depends r-magrittr:

depends r-matrix:

depends r-optparse:

depends r-paralleldist:

depends r-patchwork:

depends r-pryr:

depends r-purrr:

depends r-r.utils:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-rhpcblasctl:

depends r-roptim:

depends r-scales:

depends r-scistreer:

>=1.1.0

depends r-scistreer:

>=1.2.0,<1.3.0a0

depends r-stringr:

depends r-tibble:

depends r-tidygraph:

depends r-tidyr:

>=1.3.0

depends r-vcfr:

depends r-zoo:

requirements:

additional platforms:

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-numbat

and update with::

   mamba update r-numbat

To create a new environment, run:

mamba create --name myenvname r-numbat

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-numbat:<tag>

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

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