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.Rhistory
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?phateR::phate
?list.append
??list.append
?rename
?relocate
destiny::find_sigmas
?asinh
?Rphenograph
??Rphenograph
usethis::use_rcpp()
devtools::document()
?document
devtools::document()
warnings()
devtools::document()
devtools::document()
devtools::document()
getLoadedDLLs()
devtools::document()
pkgbuild::compile_dll()
devtools::document()
pkgbuild::compile_dll()
devtools::document()
devtools::document()
pkgbuild::compile_dll()
devtools::document()
warnings()
warnings()
devtools::document()
warnings()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::build()
devtools::document()
devtools::document()
source("~/projects/pkgs/jhuanglabHyperion/inst/doc/intro.R")
install.packages("BiocStyle")
## -----------------------------------------------------------------------------
sce <- SingleCellExperiment(list(counts=counts))
source("~/projects/pkgs/jhuanglabHyperion/inst/doc/intro.R")
BiocManager::install("BiocStyle")
install.packages("usethis")
install.packages("usethis")
source("~/projects/pkgs/jhuanglabHyperion/inst/doc/intro.R")
source("~/projects/pkgs/jhuanglabHyperion/inst/doc/apply.R")
source("~/projects/pkgs/jhuanglabHyperion/inst/doc/apply.R")
devtools::build()
devtools::build()
devtools::build()
devtools::build()
getwd()
devtools::build()
devtools::build()
devtools::document()
devtools::clean_dll()
devtools::clean_vignettes()
devtools::check_built()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::document()
devtools::check()
devtools::check()
?reducedDims
devtools::check()
?apply
devtools::check()
devtools::build()
devtools::build()
devtools::build()
devtools::build()
devtools::build()
devtools::document()
?rosnerTest
iqr
devtools::build_vignettes()
library(jhuanglabHyperion)
getwd()
knit_with_parameters("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
knit_with_parameters("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
setwd("~/projects/pkgs/jhuanglabHyperion/vignettes")
render("tutorial.Rmd", html_document())
rmarkdown::render("tutorial.Rmd", html_document())
rmarkdown::render("tutorial.Rmd")
?Rphenograph
??Rphenograph
cytofkit::Rphenograph
?Rtsne::Rtsne
?Rtsne::Rtsne
?umap::umap
?phateR::phate
?umap::umap
?uwot::umap
?gmodels::fast.prcomp
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
sce <- sce %>% pca_hyp()
sce <- sce %>% pca_hyp()
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
rmarkdown::render("~/projects/pkgs/jhuanglabHyperion/vignettes/tutorial.Rmd")
?uwot::umap
?read_csv
T && F
T && F
T }} F
T || F
T || T
T || F
T && F
T && T
F && T
F && F
T && T
scater::logNormCounts
?scater::logNormCounts
?scater::logNormCounts
?scales::oob_squish