Package index • scTenifoldKnk

Main Functions

Core analysis functions

scTenifoldKnk(): Optimized Virtual Knockout Experiment

scQC(): Single-cell quality control

Network Construction

Build gene regulatory networks

pcNetFast(): Optimized gene regulatory network construction using principal component regression

makeNetworksFast(): Optimized parallel construction of multiple gene regulatory networks

makeNetworksCpp(): Build multiple gene regulatory networks with C++ acceleration

Analysis Components

Individual analysis steps

tensorDecomposition(): Performs CANDECOMP/PARAFAC (CP) Tensor Decomposition

tensorDecompositionCpp(): CP Tensor Decomposition with C++ acceleration

manifoldAlignment(): Performs non-linear manifold alignment of two gene regulatory networks

dRegulation(): Differential regulation analysis

dRegulationCpp(): Differential regulation analysis with C++ acceleration

Utilities

Helper functions

strictDirection(): Apply directional penalty to network

strictDirectionCpp(): Enhance network directionality with C++ acceleration

knockoutGeneCpp(): Perform virtual knockout on network

sparseToDenseTranspose(): Convert sparse matrix to dense and transpose

Internal

Internal functions (CP decomposition fallback)

cpDecomposition(): Canonical Polyadic Decomposition