Package Recipe 'r-numbat'

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:

1.5.2-0, 1.5.1-0, 1.4.2-0

Depends:

on bioconductor-genomicranges >=1.58.0,<1.59.0a0
on bioconductor-ggtree >=3.14.0,<3.15.0a0
on bioconductor-iranges >=2.40.0,<2.41.0a0
on libgcc >=13
on libstdcxx >=13
on r-ape
on r-base >=4.4,<4.5.0a0
on r-catools
on r-data.table
on r-dendextend
on r-dplyr >=1.1.1
on r-ggplot2
on r-ggraph
on r-glue
on r-hahmmr >=1.0.0,<1.1.0a0
on r-igraph
on r-logger
on r-magrittr
on r-matrix
on r-optparse
on r-paralleldist
on r-patchwork
on r-pryr
on r-purrr
on r-r.utils
on r-rcpp
on r-rcpparmadillo
on r-rhpcblasctl
on r-roptim
on r-scales
on r-scistreer >=1.1.0
on r-scistreer >=1.2.0,<1.3.0a0
on r-stringr
on r-tibble
on r-tidygraph
on r-tidyr >=1.3.0
on r-vcfr
on r-zoo

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-numbat

to add into an existing workspace instead, run:

pixi add r-numbat

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-numbat

Alternatively, to install into a new environment, run:

conda create -n envname r-numbat

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-numbat:<tag>

(see r-numbat/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:

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