recipe bioconductor-cardelino

Clone Identification from Single Cell Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/cardelino.html

License:

GPL-3

Recipe:

/bioconductor-cardelino/meta.yaml

Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

package bioconductor-cardelino

Versions:

1.0.0-0

Depends:

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-ggtree >=3.6.0,<3.7.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-snpstats >=1.48.0,<1.49.0

• bioconductor-variantannotation >=1.44.0,<1.45.0

• r-base >=4.2,<4.3.0a0

• r-combinat

• r-ggplot2

• r-matrix

• r-matrixstats

• r-pheatmap

• r-vcfr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-cardelino

and update with:

conda update bioconductor-cardelino

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-cardelino:<tag>

(see bioconductor-cardelino/tags for valid values for <tag>)

Download stats

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