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DEGAS_seurat
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DeGAs seurat object |
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MHC_genes
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MHC genes |
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adjust_zstat()
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Adjust GWAS Z-statistic |
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adjust_zstat_magma()
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Adjust GWAS Z-statistic: MAGMA |
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adjust_zstat_txdb()
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Adjust GWAS Z-statistic: txdb |
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aggregate_sumstats()
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Aggregate summary statistics |
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assign_cores()
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Assign cores |
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create_DT()
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Create an interactive data table with download buttons |
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create_DimReducObject()
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Create a DimReducObject from DeGAs |
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ctd_BlueLake2018_FrontalCortexOnly
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CellTypeDataset: ctd_BlueLake2018_FrontalCortexOnly |
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extract_embeddings()
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Extract embeddings |
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extract_loadings()
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Extract loadings |
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generate_metadata()
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Generate metadata |
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get_cs2g_gwascatalog()
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Import precomputed cS2G results |
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get_cs2g_ukb()
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Import precomputed cS2G results |
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get_mhc_genes()
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Get MHC genes |
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get_phenotype_markers()
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Identify marker features for each phenotype |
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get_top_factors()
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Get the top factors |
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get_top_features()
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Plot the top feature loadings |
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get_top_phenotypes() get_top_phenotypes()
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Plot the top phenotypes |
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gwas_matrix_magma()
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Construct gene x trait matrix from MAGMA results |
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hello()
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Hello, World! |
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import_abc()
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Import ABC model predictions |
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iterate_gsea()
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Iterate gene set enrichment analysis across all traits and celltypes |
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iterate_lm()
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Iterate linear regression across all traits and celltypes |
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map_snps2genes()
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Map SNPs to genes |
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map_snps2genes_abc()
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Map SNPs to genes: ABC |
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map_snps2genes_cs2g()
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Map SNPs to genes: cS2G |
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map_snps2genes_txdb()
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Map SNPs to genes: txdb |
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plot_reduction()
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Plot reduction |
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plot_variancePartition()
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Plot variancePartition |
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reconstruct_matrix()
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Reconstruct original matrix from DeGAs components |
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regress_gene_info()
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Regress out the effect of gene attributes |
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run_gprofiler()
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Run gprofiler |
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run_mofa2()
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Run MOFA2 |
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run_pca()
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Run PCA |
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run_sparsesvd()
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Run sparse SVD |
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run_umap()
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Run UMAP |
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run_variancePartition()
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Run variancePartition |