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calc_specificity()
- Compute seismic specificity score for each gene and cell type.
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check_overlap()
- Check for overlapping genes between specificity scores and trait gene summaries from MAGMA.
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find_inf_genes()
- Calculate influential genes for a given trait and cell type using DFBETAS.
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get_ct_trait_associations()
- Calculate cell type-trait associations
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load_magma_dt()
- Check magma object / file is usable and returns it as a data.table
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plot_inf_genes()
- Plot influential genes for a given trait and cell type after running find_inf_genes().
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plot_top_associations()
- Plot the top cell type associations for a given trait.
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ra_magma
- MAGMA genes.out output for rheumatoid arthritis
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sweep_sparse()
- Similar to the base sweep function, but can be used for sparse matrices as well.
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t2d_magma
- MAGMA genes.out output for type 2 diabetes
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tmfacs_sce_small
- Small Subset of Tabula Muris FACS scRNA-seq data
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translate_gene_ids()
- Translate gene ids of a given dgeMatrix of seismic specificity scores from a given organism (e.g., mouse) to another (e.g., human) based on orthology.