recipe bioconductor-sccb2

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/scCB2.html

License:

GPL-3

Recipe:

/bioconductor-sccb2/meta.yaml

scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.

package bioconductor-sccb2

Versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

Depends:

• bioconductor-dropletutils >=1.18.0,<1.19.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-rhdf5 >=2.42.0,<2.43.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-doparallel

• r-foreach

• r-iterators

• r-matrix

• r-seurat

Required By:

Installation

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

conda install bioconductor-sccb2

and update with:

conda update bioconductor-sccb2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-sccb2:<tag>

(see bioconductor-sccb2/tags for valid values for <tag>)

Download stats

Link to this page

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