Viewing PTC Data in RStudio/Sleuth

RStudio

See Rstudio download page for instructions. Note that Shiny GUI tools are built in.

Installing Sleuth

Run the below commands one-by-one:

install.packages("BiocManager")

library(BiocManager)

BiocManager::install("rhdf5")

BiocManager::install("biomaRt")

install.packages("gridExtra")

install.packages("devtools")

devtools::install_github("pachterlab/sleuth")

Loading packages

library(rhdf5)

library(sleuth)

library(biomaRt)

library(gridExtra)

Importing the prepared PTC dataset

1. Set working directory to location of the downloaded so.rds setwd(/path/to/directory/)

2. Save read the RDS file as "so" so <-readRDS('so.rds')

3. Visualize the data sleuth_live(so)

User Interface

Sleuth Live Example:

Tips:

• Case matters. Human gene names should be capitalized
• Select "Gene_Name" from the dropdown menu as shown above when searching for single-gene expression across samples.
• Use the top menu to select from other pre-prepared plots and figures.
• This object can be used to manipulate data, export tables and create new figures in the R commandline (outside of sleuth_live).