diff --git a/R/listSims.R b/R/listSims.R index 359e8f0ceca22ca0dd01e3a4eece273432ab1846..51fb3ff91491b274ff28f5e82d0187bb523c63ba 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 7da353f10dddc7efc64060ee37b857127c048215..cd4c1f15af8c7b76d2e5256036d63835e03d3ba6 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`'