---
title: 'DESeq2 analysis'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo
      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = opt$echo,
  error = TRUE
)
```


## User input

```{r 'user input'}
df = data.frame(name = names(opt)[-1],
                value = unlist(opt))
df
```


## Count Matrix

```{r 'count matrix'}
count_data = read.table(opt$count_data)
head(count_data, 10)
```

```{r 'ste[ 2'}

```