Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e
インストールする前に、エージェントに与えられる指示の中身を確認できます。
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("basilisk")BasiliskEnvironment to freeze dependencies.scikit-learn's TruncatedSVD) on R matrices safely in an isolated process via basiliskRun.createLocalBasiliskEnv and basiliskRun to prevent dependency clashes.reticulate directly because basilisk is primarily intended for package developers to freeze dependencies.matrix(rnorm(1000), ncol=10)) that are amenable to serialization.basiliskRun.basilisk; depends entirely on the downstream Python module being called.BasiliskEnvironment.BasiliskEnvironment."pandas==2.2.3") to install.basiliskRun.basiliskRun by passing a store environment.clearExternalDir to remove only obsolete environments."scikit-learn==1.6.1") in BasiliskEnvironment to future-proof the installation.basiliskStart and basiliskStop (via on.exit()) to manage the process context when executing basiliskRun.basiliskRun is a pure R object, not a reticulate binding or pointer to external memory.::) inside the function passed to basiliskRun.basiliskRun.reticulate bindings to Python objects causes invalid pointer errors when transferred back to the parent process; fix this by returning only pure R objects.BASILISK_EXTERNAL_DIR environment variable to a shorter path.clearExternalDir to forcibly clear obsolete environments.basilisk.This skill is the knowledge layer — when, why, and how to use basilisk. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
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概要と使いどころ
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
日本語の概要は準備中です。原文の説明を表示しています。
This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
日本語の概要は準備中です。原文の説明を表示しています。
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
日本語の概要は準備中です。原文の説明を表示しています。
apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
日本語の概要は準備中です。原文の説明を表示しています。
ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
日本語の概要は準備中です。原文の説明を表示しています。
AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
日本語の概要は準備中です。原文の説明を表示しています。