From a9848416da9527af36553921fce5427399f836d0 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 5 Oct 2017 12:34:02 +1100
Subject: [PATCH] Add ZINB-WaVE simulation to lists
---
R/listSims.R | 7 ++++++-
_pkgdown.yml | 3 +++
2 files changed, 9 insertions(+), 1 deletion(-)
diff --git a/R/listSims.R b/R/listSims.R
index a7085b7..cbf18ef 100644
--- a/R/listSims.R
+++ b/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)),
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 0bf1df1..6680559 100644
--- a/_pkgdown.yml
+++ b/_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:
--
GitLab