recipe bioconductor-scope

A normalization and copy number estimation method for single-cell DNA sequencing

Homepage

https://bioconductor.org/packages/3.11/bioc/html/SCOPE.html

License

GPL-2

Recipe

/bioconductor-scope/meta.yaml

Whole genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy number profiles at the cellular level. This circumvents the averaging effects associated with bulk-tissue sequencing and has increased resolution yet decreased ambiguity in deconvolving cancer subclones and elucidating cancer evolutionary history. ScDNA-seq data is, however, sparse, noisy, and highly variable even within a homogeneous cell population, due to the biases and artifacts that are introduced during the library preparation and sequencing procedure. Here, we propose SCOPE, a normalization and copy number estimation method for scDNA-seq data. The distinguishing features of SCOPE include: (i) utilization of cell-specific Gini coefficients for quality controls and for identification of normal/diploid cells, which are further used as negative control samples in a Poisson latent factor model for normalization; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the Poisson generalized linear models, which accounts for the different copy number states along the genome; (iii) a cross-sample iterative segmentation procedure to identify breakpoints that are shared across cells from the same genetic background.

package bioconductor-scope

(downloads) docker_bioconductor-scope

Versions

1.0.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-scope

and update with:

conda update bioconductor-scope

or use the docker container:

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

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