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annotate_links_with_ccans()
Annotate co-accessible links with CCAN membership and return GInteractions
annotate_tss()
Annotate regulatory elements overlapping transcription start sites (TSS)
annotate_with_coaccessibility()
Annotate Regulatory Elements with Gene Targets Using Co-Accessibility Links
annotate_with_nearest()
Annotate regions with nearest gene and promoter information
combine_gex_da()
Combine Differential Expression Results Across Cell Types
entropy_getsi()
Compute normalized entropy of GETSI scores
entropy_retsi()
Compute entropy of RETSI scores per regulatory region
get_ccan()
Extract CCAN membership from links for a given GRanges object
get_main_seqlevels()
Get main chromosomes from a GRanges or TxDb, filtering alt/hap/random/etc.
get_promoters()
Get Promoter Regions with Optional Filtering for Protein-Coding Genes Extracts promoter regions (±2kb default) from a TxDb object, optionally restricting to protein-coding genes and retaining only primary chromosomes (using a robust internal filter). Gene symbols and types are added using an AnnotationDbi object.
get_targets_links()
Link regulatory elements to genes based on shared CCAN membership
getsi()
Compute GETSI scores on RNA data
link_spicey_coaccessible()
Link RETSI peaks with GETSI values from coaccessibility
link_spicey_nearest()
Link RETSI peaks with GETSI values from nearest genes
retsi()
Compute RETSI scores for differential chromatin accessibility data
run_spicey()
Run the full SPICEY pipeline
spicey_getsi()
Compute GETSI scores and entropy from RNA-seq data
spicey_retsi()
Compute RETSI scores and entropy for scATAC-seq regulatory elements