params <-
list(isSlides = "no")
## ----include=FALSE------------------------------------------------------------
suppressPackageStartupMessages(require(knitr))
knitr::opts_chunk$set(echo = TRUE, tidy = T)
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides != "yes"){
cat("# Loupe Browser
---
"
)
}
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# 10X scRNAseq datasets
---
"
)
}else{
cat("# 10X scRNAseq datasets
---
"
)
}
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Clustering
---
"
)
}else{
cat("# Clustering
---
"
)
}
## ----out.width = "60%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/bad_cluster.png")
## ----out.width = "70%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/custom_Group.png")
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Diffential Expression
---
"
)
}else{
cat("# Diffential Expression
---
"
)
}
## ----out.width = "70%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/diff.png")
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Features
---
"
)
}else{
cat("# Features
---
"
)
}
## ----out.width = "70%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/coexp.png")
## ----out.width = "70%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/cross_comparison.png")
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Custom Groups
---
"
)
}else{
cat("# Custom Groups
---
"
)
}
## ----out.width = "60%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/min.png")
## ----out.width = "60%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/savebar.png")
## ----out.width = "60%", echo=F------------------------------------------------
knitr::include_graphics("./imgs/freehand2.png")
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Reanalyze
---
"
)
}else{
cat("# Reanalyze
---
"
)
}
## ----results='asis',include=TRUE,echo=FALSE-----------------------------------
if(params$isSlides == "yes"){
cat("class: inverse, center, middle
# Import/Export
---
"
)
}else{
cat("# Import/Export
---
"
)
}
## ----eval=F-------------------------------------------------------------------
# library(loupeR)
#
# create_loupe_from_seurat(seu_obj,
# output_dir = "loupe",
# output_name = "scRNA_annotated_Igfilter")