In mcanouil/insane: INsulin Secretion ANalysEr

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-",
  out.width = "100%"
)

knitr::include_graphics(path = "insane.png")

Installation

# Install insane from CRAN:
install.packages("insane")

# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("mcanouil/insane")

library("insane")
go_insane()

Overview

The Shiny (R package) application insane (INsulin Secretion ANalysEr) provides a web interactive tool to import experiments of insulin secretion using cell lines such as EndoC-βH1.

Excel Template

An Excel template is provided within the app to help users import their experiments in an easy way.

The App

insane provides a user-friendly interface which can handle several projects separately.

knitr::include_graphics("README-app_001.png")

Technical Quality-Control

insane performs technical quality-control of the optical density measured in each steps of the experiments:

• blank (BLANK),
• lysat (LYSATE),
• supernatant (SUPERNATANT1 and SUPERNATANT2).

This technical quality-control step checks:

• the variability among the duplicated optical density measures of each samples;
• the variability in the blank curves (intercept and slope estimates) among all experiments in a project.

knitr::include_graphics("README-app_002.png")

Statistical analyses

insane performs statistical analyses of the experimental conditions, e.g., one silenced gene (siGENE) compared to an insulin secretion reference (siNTP) in two stimulation conditions (Glc and Glc + A).

Conditions are compared using a linear regression with Date and Operator as covariates (if needed) to control for heterogeneity.

• Using all experiments in the selected project

  • Boxplot version

    r knitr::include_graphics("README-app_003.png")

  • Histogram version

    r knitr::include_graphics("README-app_004.png")

• Using some of the experiments in the selected project

  r knitr::include_graphics("README-app_005.png")

If and when some experiments are failing any of the technical quality-controls, a summary of the issues regarding the selected experiments can be displayed using the button Show Issues in the Selected Experiments.

knitr::include_graphics("README-app_006.png")

List of Outliers (Issues Detected)

A comprehensive list of all issues detected in the selected project is available in an Outliers tab.

knitr::include_graphics("README-app_007.png")

Note: The Outliers tab is displayed only if there is at least one issue in the selected project.

mcanouil/insane documentation built on Jan. 2, 2025, 3:11 a.m.