---
title: "countfitteR package - an overview"
author: "Jarosław Chilimoniuk, Alicja Gosiewska, Jadwiga Słowik, Stefan Rödiger, Michał Burdukiewicz"
date: "`r Sys.Date()`"
output: 
  rmarkdown::html_vignette:
    number_sections: true
    toc: true
    toc_depth: 4
header-includes:
    - \usepackage[font={small}]{caption}
bibliography: countfitteR.bib
# bibliography: bib.json
# nocite: '@*'
classoption: a4paper
vignette: >
  %\VignetteIndexEntry{countfitteR package - an overview}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

# Introduction

**countfitteR** is a R package and shiny app designed to perform analysis of count data. 
This vignette covers important features and data sets of the app. 
We extended our automatized imaging platform [@rodiger_highly_2013, 
@willitzki_new_2012] for a multiparametric analysis of cell damage (DNA double 
strand breaks) [@reddig_dna_2018, @rodiger_quantification_2018]. 
Digital image analysis of the DSB biomarkers gamma H2AX was used to describe the 
alteration of the cell phenotype.

# Data sets

```{r eval=TRUE, echo=TRUE, warning=FALSE}
# Load countfitteR package
library(countfitteR)

# Assign the csv file to filename
data("case_study")

processed_counts <- process_counts(case_study)

fit_counts(processed_counts, model = "all")
```



# References