Package: BiocSklearn 1.29.0

Vince Carey

BiocSklearn: interface to python sklearn via Rstudio reticulate

This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.

Authors:Vince Carey [cre, aut]

BiocSklearn_1.29.0.tar.gz
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BiocSklearn.pdf |BiocSklearn.html✨
BiocSklearn/json (API)
NEWS

# Install 'BiocSklearn' in R:

install.packages('BiocSklearn', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:BiocSklearn-1.27.2(bioc 3.20)BiocSklearn-1.26.1(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

statisticalmethod dimensionreduction infrastructure

4.44 score 11 scripts 222 downloads 12 exports 41 dependencies

Last updated 22 days agofrom:8c69d92d52. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 30 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 30 2024
R-4.4-mac	OK	Oct 30 2024
R-4.3-win	OK	Oct 30 2024
R-4.3-mac	OK	Oct 30 2024

Exports:getTransformed h5mat H5matref SkDecomp skIncrPartialPCA skIncrPCA skIncrPCA_h5 skIncrPPCA skKMeans skPartialPCA_step skPCA skPWD

Dependencies:abind askpass basilisk basilisk.utils Biobase BiocGenerics crayon curl DelayedArray dir.expiry filelock GenomeInfoDb GenomeInfoDbData GenomicRanges here httr IRanges jsonlite lattice Matrix MatrixGenerics matrixStats mime openssl png R6 rappdirs Rcpp RcppTOML reticulate rlang rprojroot S4Arrays S4Vectors SparseArray SummarizedExperiment sys UCSC.utils withr XVector zlibbioc

BiocSklearn -- exposing python Scikit machine learning elements for Bioconductor

Vincent J. Carey, stvjc at channing.harvard.edu, Shweta Gopaulakrishnan, reshg at channing.harvard.edu, Samuela Pollack, spollack at jimmy.harvard.edu

Rendered fromBiocSklearn.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-01-27
Started: 2017-07-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
create a file connection to HDF5 matrix	h5mat
obtain an HDF5 dataset reference suitable for handling as numpy matrix	H5matref
constructor for SkDecomp	SkDecomp
container for sklearn objects and transforms	getTransformed getTransformed,SkDecomp-method SkDecomp-class
use basilisk discipline to perform partial (n_components) incremental (chunk.size) PCA with scikit.decomposition	skIncrPartialPCA
use sklearn IncrementalPCA procedure	skIncrPCA
demo of HDF5 processing with incremental PCA/batch_size/fit_transform	skIncrPCA_h5
optionally fault tolerant incremental partial PCA for projection of samples from SummarizedExperiment	skIncrPPCA skIncrPPCA,SummarizedExperiment-method
interface to sklearn.cluster.KMeans using basilisk discipline	skKMeans
take a step in sklearn IncrementalPCA partial fit procedure	skPartialPCA_step
use sklearn PCA procedure	skPCA
use sklearn pairwise_distances procedure	skPWD