From dbac87deddf981f3b70658a9133bfbaccc355cab Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Sun, 1 Oct 2017 16:05:26 +1100
Subject: [PATCH] Add mfa to lists
---
R/listSims.R | 14 ++++++++++----
_pkgdown.yml | 3 +++
2 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/R/listSims.R b/R/listSims.R
index 359e8f0..51fb3ff 100644
--- a/R/listSims.R
+++ b/R/listSims.R
@@ -15,7 +15,8 @@ listSims <- function(print = TRUE) {
sims <- list(c("Splat", "splat", "", "",
"The Splat simulation generates means from a gamma
distribution, adjusts them for BCV and generates counts from
- a gamma-poisson. Dropout can be optionally added."),
+ a gamma-poisson. Dropout and batch effects can be optionally
+ added."),
c("Splat Single", "splatSingle", "", "",
"The Splat simulation with a single population."),
c("Splat Groups", "splatGroups", "", "",
@@ -46,12 +47,17 @@ listSims <- function(print = TRUE) {
"kdkorthauer/scDD",
"The scDD simulation samples a given dataset and can
simulate differentially expressed and differentially
- distributed genes between two conditions."))
+ distributed genes between two conditions."),
+ c("mfa", "mfa", "10.12688/wellcomeopenres.11087.1",
+ "kieranrcampbell/mfa",
+ "The mfa simulation produces a bifurcating pseudotime
+ trajectory. This can optionally include genes with transient
+ changes in expression and added dropout."))
sims.table <- data.frame(Name = rep(NA, length(sims)),
Prefix = rep(NA, length(sims)),
DOI = rep(NA, length(sims)),
- Github = rep(NA, length(sims)),
+ GitHub = rep(NA, length(sims)),
Description = rep(NA, length(sims)))
for (idx in seq_along(sims)) {
@@ -65,7 +71,7 @@ listSims <- function(print = TRUE) {
for (idx in seq_len(nrow(sims.table))) {
sim <- as.character(sims.table[idx, ])
cat(sim[1], paste0("(", sim[2], ")"), "\n")
- cat("DOI:", sim[3], "\t", "Github:", sim[4], "\n")
+ cat("DOI:", sim[3], "\t", "GitHub:", sim[4], "\n")
cat(sim[5], "\n\n")
}
}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 7da353f..cd4c1f1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -12,6 +12,7 @@ reference:
- '`getParams`'
- '`Lun2Params`'
- '`LunParams`'
+ - '`MFAParams`'
- '`newParams`'
- '`Params`'
- '`SCDDParams`'
@@ -24,6 +25,7 @@ reference:
contents:
- '`lun2Estimate`'
- '`lunEstimate`'
+ - '`mfaEstimate`'
- '`scDDEstimate`'
- '`simpleEstimate`'
- '`splatEstBCV`'
@@ -37,6 +39,7 @@ reference:
contents:
- '`lun2Simulate`'
- '`lunSimulate`'
+ - '`mfaSimulate`'
- '`scDDSimulate`'
- '`simpleSimulate`'
- '`splatSimBatchCellMeans`'
--
GitLab