Merge branch 'zinb'

* zinb:
  Add ZINB-WaVE simulation to lists

R/listSims.R

@@ -56,7 +56,12 @@ listSims <- function(print = TRUE) {
                  c("PhenoPath", "pheno", "10.1101/159913",
                    "kieranrcampbell/phenopath",
                    "The PhenoPath simulation produces a pseudotime trajectory
-                   with different types of genes."))
+                   with different types of genes."),
+                 c("ZINB-WaVE", "zinb", "10.1101/125112",
+                   "drisso/zinbwave",
+                   "The ZINB-WaVE simulation simulates counts from a
+                   sophisticated zero-inflated negative-binomial distribution
+                   including cell and gene-level covariates."))
 
     sims.table <- data.frame(Name        = rep(NA, length(sims)),
                              Prefix      = rep(NA, length(sims)),

_pkgdown.yml

@@ -21,6 +21,7 @@ reference:
       - '`SplatParams`'
       - '`setParam`'
       - '`setParams`'
+      - '`ZINBParams`'
   - title: Estimation
     desc: Functions for estimating parameters
     contents:
@@ -36,6 +37,7 @@ reference:
       - '`splatEstLib`'
       - '`splatEstMean`'
       - '`splatEstOutlier`'
+      - '`zinbEstimate`'
   - title: Simulation
     desc: Functions for simulating datasets
     contents:
@@ -55,6 +57,7 @@ reference:
       - '`splatSimLibSizes`'
       - '`splatSimTrueCounts`'
       - '`splatSimulate`'
+      - '`zinbSimulate`'
   - title: Comparison functions
     desc: Functions for comparing datasets
     contents: