Package index • nicheDE

Creating an Average Expression Matrix

Functions for Creating the Average Expression Matrix

CreateLibraryMatrix(): CreateLibraryMatrix

CreateLibraryMatrixFromSeurat(): CreateLibraryMatrixFromSeurat

Creating a Niche-DE Object

Functions for Creating a Niche-DE Object

CreateNicheDEObject(): CreateNicheDEObject

CreateNicheDEObjectFromSeurat(): CreateNicheDEObjectFromSeurat

Filter_NDE(): Filter_NDE

MergeObjects(): MergeObjects

Calculating the Effective Niche and Performing Niche-DE

Functions for Calculating the Effective Niche and Performing Niche-DE

CalculateEffectiveNiche(): CalculateEffectiveNiche

CalculateEffectiveNicheLargeScale(): CalculateEffectiveNiche

niche_DE(): Niche_DE

niche_DE_no_parallel(): Niche_DE

Downstream Analysis

Functions for Performing Downstream Analysis

get_niche_DE_genes(): Getniche genes for the given index and niche cell types at the desired test.level

niche_DE_markers(): Get Niche-DE marker genes(test)

niche_LR_cell(): Perform Niche-LR (Ligand receptor analysis) on single cell level data

niche_LR_spot(): Perform Niche-LR (Ligand receptor analysis) on spot level data