recipe bioconductor-pcamethods

A collection of PCA methods

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-pcamethods/meta.yaml

Links:

biotools: pcamethods, doi: 10.1093/bioinformatics/btm069

Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.

package bioconductor-pcamethods

Versions:

1.90.0-1,  1.90.0-0,  1.86.0-2,  1.86.0-1,  1.86.0-0,  1.84.0-0,  1.82.0-1,  1.82.0-0,  1.80.0-0, 

1.90.0-1,  1.90.0-0,  1.86.0-2,  1.86.0-1,  1.86.0-0,  1.84.0-0,  1.82.0-1,  1.82.0-0,  1.80.0-0,  1.78.0-0,  1.76.0-1,  1.74.0-0,  1.72.0-0,  1.70.0-0,  1.68.0-0,  1.64.0-2,  1.64.0-1,  1.64.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-mass

• r-rcpp >=0.11.3

Required By:

• bioconductor-multibac

• bioconductor-matrixqcvis

• bioconductor-somaticsignatures

• bioconductor-destiny

• bioconductor-scde

• bioconductor-consensusde

• bioconductor-phosr

• bioconductor-fraser

• bioconductor-msnbase

• bioconductor-mai

• r-ramclustr

• bioconductor-deconrnaseq

• bioconductor-outrider

• r-imputelcmd

• r-metaboanalyst

• r-velocyto.r

• bioconductor-msprep

• bioconductor-autonomics

• r-diffcorr

• bioconductor-pmp

• r-crmn

Installation

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

conda install bioconductor-pcamethods

and update with:

conda update bioconductor-pcamethods

or use the docker container:

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

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

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