TieDIE

TieDIE is a pathway reconstruction algorithm which TODO. See the original paper and SPRAS’s fork of the codebase: https://github.com/Reed-CompBio/TieDIE.

TieDIE takes several optional parameters:

• s: (int, default 1) Network size control factor

• d_expr: List of significantly differentially expressed genes, along with log-FC or FC values (i.e. by edgeR for RNA-Seq or SAM for microarray data. Generated by a sample-dichotomy of interest.)

• a: (int) Linker Cutoff (overrides the Size factor)

• c: (int, default 3) Search depth for causal paths

• p: (int, default 1000) Number of random permutations performed for significance analysis

• pagerank: (boolean, default false) uses PageRank for diffusion

• all_paths: (boolean, default false) Use all paths instead of only causal paths