Package index • AEGIS

Data input

load_10x_lymphnode(): Load the 10x Human Lymph Node Visium dataset as a Seurat object
load_10x_spatial_set(): Load a set of 10x spatial datasets
merge_spatial_seurat_list(): Merge a list of spatial Seurat objects
aegis_example: Example Seurat object derived from Human Lymph Node data
aegis_default_markers(): Default marker list used by AEGIS MVP
align_deconv_to_seurat(): Align a deconvolution matrix to Seurat spot order
read_deconv_table(): Read a generic deconvolution result table
read_rctd(): Read RCTD deconvolution outputs
read_spotlight(): Read SPOTlight deconvolution outputs
read_cell2location(): Read cell2location deconvolution outputs
read_card(): Read CARD deconvolution outputs
read_spatialdwls(): Read SpatialDWLS deconvolution outputs
read_stereoscope(): Read stereoscope deconvolution outputs
read_destvi(): Read DestVI deconvolution outputs
read_tangram(): Read Tangram mapping-derived composition outputs
read_stdeconvolve(): Read STdeconvolve outputs
read_dstg(): Read DSTG deconvolution outputs
read_stride(): Read STRIDE deconvolution outputs

run_aegis(): Run the standard AEGIS workflow with one function
run_deconvolution() run_aegis_full() run_spotlight() run_card() run_rctd() run_cell2location() run_destvi() run_tangram() run_stereoscope(): Unified deconvolution orchestration and method runners
get_supported_methods(): List supported deconvolution methods and execution modes
as_aegis(): Construct an AEGIS object
as_aegis_multi(): Construct a multi-sample AEGIS object
is_aegis(): AEGIS analysis object
is_aegis_multi(): Check if object is an AEGIS multi-sample object
split_aegis_by_sample(): Split an AEGIS object by sample
summarize_by_sample(): Summarize AEGIS results by sample
simulate_deconv_results(): Simulate deconvolution results for a Seurat spatial object

audit_basic(): Run basic quality audits on deconvolution matrices
audit_marker(): Run marker-based concordance audit
audit_spatial(): Run spatial smoothness audit
compare_methods(): Compare deconvolution methods
score_methods(): Score deconvolution methods from available audit evidence
rank_methods(): Rank methods from evidence dimensions
compute_consensus(): Compute consensus deconvolution profile

plot_audit(): Plot audit outputs
plot_compare(): Plot method comparison and consensus outputs
plot_method_ranking(): Plot method ranking summary
plot_disagreement_map(): Plot spot-level consensus disagreement map
plot_consensus_confidence(): Plot spot-level consensus confidence map
render_report(): Render an AEGIS HTML report
render_report_batch(): Render one report per sample
build_aegis_example_data(): Build and save example data from raw Human Lymph Node files