recipe bioconductor-dino

Normalization of Single-Cell mRNA Sequencing Data

Homepage

https://bioconductor.org/packages/3.14/bioc/html/Dino.html

License

GPL-3

Recipe

/bioconductor-dino/meta.yaml

Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.

package bioconductor-dino

Versions

1.0.0-0

Depends

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-biocsingular >=1.10.0,<1.11.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-scran >=1.22.0,<1.23.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-matrix

• r-matrixstats

• r-seurat

Required By

Installation

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

conda install bioconductor-dino

and update with:

conda update bioconductor-dino

or use the docker container:

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

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

Download stats

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