Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes f
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("zellkonverter")SingleCellExperiment from a .h5ad file using readH5AD.SingleCellExperiment to a .h5ad file using writeH5AD.SingleCellExperiment and Python AnnData objects in memory using SCE2AnnData and AnnData2SCE.AnnDataDependencies.SeuratDisk or convert to SingleCellExperiment first, because zellkonverter strictly interfaces with SingleCellExperiment.basilisk directly, as zellkonverter uses it internally but isn't a general-purpose environment manager..h5ad file on disk for reading.SingleCellExperiment object in R for writing or conversion.AnnData object in Python (via reticulate) for in-memory conversion..h5ad file in readH5AD or output destination in writeH5AD.readH5AD.anndata to return dependencies for in AnnDataDependencies (e.g., "0.7.6").zellkonverterAnnDataEnv() in basiliskRun.basiliskRun with zellkonverterAnnDataEnv() to safely execute Python code on AnnData objects within a controlled environment.AnnDataDependencies() if you are a package developer to guarantee you are using the same versions of Python packages as zellkonverter.setZellkonverterVerbose(TRUE) if you want to monitor large conversions.basilisk to set up the Python environment before using SCE2AnnData or AnnData2SCE..h5ad files correctly. Fix: Check required versions with AnnDataDependencies() to ensure compatibility..h5ad files. Fix: Set verbose = TRUE in readH5AD to display progress messages.zellkonverter wraps specifically for AnnData..h5ad files.This skill is the knowledge layer — when, why, and how to use zellkonverter. 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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The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
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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
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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
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apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
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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).
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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
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