Package index
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AIDA_QCREF - Test data for QC of reference genes.
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Gene_QC() - QC to remove potential escapee genes from reference gene set
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XCI_ref - A dataframe (tibble) containing X chromosome inactivation (XCI) status.
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make_QC_gene_table() - Create a dataframe for QC of candidate reference genes
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make_QCed_df() - Quality Control of the input data frame (for internal use only)
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make_per_SNP_sample_df() - Generate a per-SNP summary of the number of samples (for internal use only)
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make_pseudobulk_refSNP() - Create pseudobulk data for reference SNPs (for internal use only)
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multiome_ASE_df - Test single-cell allele-specific expression data for scLinaX.
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multiome_ATAC_ASE_data - Test single-cell allele-specific chromatin accessibility data for scLinaX-multi.
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multiome_Annotation - Test data for QC of reference genes.
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multiome_peak_data - Test peak data for scLinaX-multi.
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run_RefGeneQC() - Run Gene Quality Control (QC) function
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run_clustering() - Generate pseudobulk profiles for individuals and calculate correlations (for internal use only)
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run_grouping() - Define groups for SNP alleles (for internal use only)
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run_scLinaX() - Run scLinaX analysis for all samples
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run_scLinaX_multi() - Run scLinaX-multi using the scATAC data and output from scLinaX (Currently, only single sample mode is implemented).
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summarize_QC_gene_table() - Summarize the dataframe generated for QC
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summarize_scLinaX() - Summarize scLinaX results (return per-individual summary)
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summarize_scLinaX_multi() - Summarize scLinaX-multi results