diag_kernel | Make diagonal kernel matrix |
edgelist2graph | Transform a data frame edge list into an 'igraph' graph |
ezpermutations | Resample sample labels for permutation testing |
Gmat2gmt | Transform analyte-by-pathway matrix into list compatible with... |
gmt2Gmat | Transform list from GMT into feature-by-pathway matrix |
graph2kernel | Transform an 'igraph' graph into a p-step random walk kernel |
match_mats | Expand kernel to match features in object and pathway matrix |
mat_pow | Calculate power of a matrix |
neighbor_nms | Get names of nodes' neighbors |
opt_binom_n | Find minimal binomial N that ensures 'ezpermutations' obtains... |
pants | Pathway analysis via network smoothing (Pants) |
p_ecdf | Estimate p-value from simulations |
plot_pwy | Plot network diagram for a pathway |
sapply_by_ncores | Sapply by number of cores |
score_features | Score features using ezlimma and score_fcn |
select_ntop_per_pwy | Select top drivers for a pathway |
sif2edgelist | Clean Pathway Commons SIF file |
sim_pants | Simulate 'pants' to estimate size & power |
sim_pants_mediation | Simulate 'pants' with mediation to estimate size & power |
SMPDB2Gmat | Transform SMPDB protein and/or metabolite pathway data frames... |
subset_gmat | Subset pathway inclusion matrix based on size |
write_pants_xl | Write Excel XLSX file with links to CSVs |
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