recipe bioconductor-deconvr

Simulation and Deconvolution of Omic Profiles

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-deconvr/meta.yaml

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

package bioconductor-deconvr

Versions:

1.4.0-0,  1.0.1-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-methylkit >=1.24.0,<1.25.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-assertthat

• r-base >=4.2,<4.3.0a0

• r-data.table >=1.14.0

• r-dplyr >=1.0.7

• r-e1071 >=1.7.9

• r-foreach >=1.5.1

• r-magrittr >=2.0.1

• r-mass

• r-matrixstats >=0.61.0

• r-nnls >=1.4

• r-quadprog >=1.5.8

• r-rsq >=2.2

• r-tidyr >=1.1.3

Required By:

Installation

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

conda install bioconductor-deconvr

and update with:

conda update bioconductor-deconvr

or use the docker container:

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

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

Download stats

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