A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.
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Correct and fine-tune noisy or mislabeled cell type annotations in single-cell RNA-seq data using semi-supervised learning.
library(scReClassify)
library(SingleCellExperiment)
# Load pre-processed SingleCellExperiment data
data("gse87795_subset_sce")
dat <- gse87795_subset_sce
# Perform dimension reduction using matPCs to retain PCs explaining >= 70% variance
reducedDim(dat, "matPCs") <- matPCs(dat, assay = "logNorm", 0.7)
Input: A SingleCellExperiment object containing log-normalized expression data. Output: A SingleCellExperiment object with a dimension-reduced matrix stored in reducedDim(dat, "matPCs").
matPCs to select principal components explaining at least 70% of the variance.SingleCellExperiment object.scran or Seurat because scReClassify is a post hoc semi-supervised tool that requires initial cell type annotations.scReClassify relies on the adaSampling algorithm which requires a set of initial (potentially noisy) labels.SingleCellExperiment object or a matrix.colData (e.g., cellTypes).logNorm assay) is required for dimension reduction.SingleCellExperiment object to perform dimension reduction on.matPCs.matPCs to automatically select the number of principal components that explain at least 70% of the variance.matPCs on a SingleCellExperiment without specifying the correct assay name, which will result in an error if the default assay is missing. Fix by explicitly setting the assay parameter (e.g., assay = "logNorm").Seurat for general single-cell classification and clustering.scater for standard PCA and dimension reduction.scran for unsupervised cell clustering.还没有评价。欢迎分享你的使用感受。
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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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