Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("SingleR")HumanPrimaryCellAtlasData()).scran instead because SingleR requires known labels).Seurat instead because SingleR automates this using a reference).SingleR().normalizeRnaCounts.se())."wilcox" for single-cell references).SingleR().normalizeRnaCounts.se().plotScoreHeatmap() and plotDeltaDistribution().pruneScores().plotMarkerHeatmap().normalizeRnaCounts.se()).de.method="wilcox" to consider variance of expression across cells).pruneScores() to replace low-quality assignments with NA).Seurat (for manual marker gene definition and cluster interpretation).scmap (for projection-based single-cell annotation).This skill is the knowledge layer — when, why, and how to use singler. 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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