I add an additional css as shown in http://rpubs.com/stevepowell99/floating-css

via :

---
output:
  BiocStyle::html_document:
    css: my.css
---

and 

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown(css.files = c('my.css'))
```

But it fail to generate a html as expected. The table of content is still in the beginning of the main text.

Is it possible to generate toc floating in left hand side with BiocStyle?

Dear Guangchuang,

this should in principle be possible. Please note that if you are specifying the CSS file in the header you shouldn't repeat it in the argument to BiocStyle::markdown, and you probably need to explicitly set toc: yes

Please try the following code which works for me:

---
output:
  BiocStyle::html_document:
    toc: yes
    css: custom.css
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
```

custom.css

#TOC {
position: fixed;
left: 0;
top: 0;
width: 200px;
height: 100%;
overflow:auto;
}

Best,

Andrzej