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IDC_summary_scEpigenomics
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A data.frame containing the summary of differential markers for scEpigenomics dataset
(Paired-Tag - H3K27ac) |
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IDC_summary_scRNA
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A data.frame containing the summary of differential markers for scRNA dataset
(Paired-Tag - scRNA) |
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Seu
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A Seurat object containing the scRNA part of Paired-Tag dataset. (Paired-Tag - scRNA) |
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calculate_FDR_scEpigenomics()
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Calculate FDR for SingleCellExperiment object |
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create_pseudobulk_mat_Seu()
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Create Pseudo-Bulk Matrice from scRNA clusters & replicates |
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differential_ChromSCape()
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Differential analysis with ChromSCape (differential activation) |
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differential_Seurat()
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Differential function Seurat (wilcoxon) |
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differential_edgeR_pseudobulk_LRT()
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Pseudo-bulk differential analysis with edgeR (LRT) |
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find_differentiated_clusters()
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Find Differentiated Clusters |
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iterative_differential_clustering()
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iterative_differential_clustering |
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plot_cluster_network()
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Plot Iterative Differential Clustering network |
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processing_ChromSCape()
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Normalize and run PCA with ChromSCape (LSI) |
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processing_Seurat()
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Normalize and run PCA with Seurat |
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scExp
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A SingleCellExperiment object containing the scH3K27ac part of Paired-Tag
dataset. (Paired-Tag - H3K27ac) |
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top_differential_markers.SingleCellExperiment()
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Retrieve Top differential markers |