- 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:
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-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-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¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-deconvr/README.html)