1. Overview ¶

최근 comprehensive genomic profiling을 사용한 대규모 코호트 연구들에 따르면 90%가 유용한 alteration을 가지고 있다고 보고되고 있다cite{Priestley:2019bp}. 엔젠바이오는 연구자들을 돕기 위해 323개의 암관련 유전자 (225 coding exon, 98 hotspot cover)를 분석하는 ONCOaccuPanel을 제공한다. small nucleotide variants(SNVs), insertions/deletions(indels), copy-number variations(CNVs), splice variants, fusions과 함께 최근 다수의 genomic loci 분석을 기반으로 하는 tumor mutational burden(TMB) and microsatellite instability(MSI) 분석을 제공한다.

1: A numerical footnote.
2: 모든 암종에 대해서 기준값 (>23 Muts/Mb)을 제공하지만, TMB의 high/low는 암 종마다 기준값이 달라질 수 있음

참고

로그인 창이 나타나지 않거나 로그인 버튼을 눌러도 연결되지 않는 경우에는 인터넷 또는 기관 내부망(인트라넷) 연결이 활성화 되었는지 확인하거나, 아이디 및 비밀번호를 올바르게 입력했는지 확인한다.

경고

선택한 암종에 따라 해석(interpreation)의 tier 정보가 달라진다.
선택한 암종에 따라 white list가 달라진다.

NGS를 수행한 RUN 이름을 입력한다.
《Local Fastq Files》을 선택하여 로컬 컴퓨터의 FASTQ 파일 또는 《Server Fastq Files》를 선택1하여 원격지의 FASTQ 파일을 선택한다.
분석할 FASTQ 파일을 선택한 후, 열기 버튼을 클릭한다.

This theme provides a responsive Material Design theme for Sphinx documentation. It derives heavily from Material for MkDocs , and also uses code from Guzzle Sphinx Theme .

There are two methods to alter the theme. The first, and simplest, uses the options exposed through html_theme_options in conf.py . This site’s options are:

         html_theme_options = {
    'base_url': 'http://bashtage.github.io/sphinx-material/',
    'repo_url': 'https://github.com/bashtage/sphinx-material/',
    'repo_name': 'Material for Sphinx',
    'google_analytics_account': 'UA-XXXXX',
    'html_minify': True,
    'css_minify': True,
    'nav_title': 'Material Sphinx Demo',
    'logo_icon': '&#xe869',
    'globaltoc_depth': 2
}

        

The complete list of options with detailed explanations appears in theme.conf .

1.1. Configuration Options ¶

nav_title

Set the name to appear in the left sidebar/header. If not provided, uses html_short_title if defined, or html_title.

touch_icon

Path to a touch icon, should be 152x152 or larger.

google_analytics_account

Set to enable google analytics.

repo_url

Set the repo url for the link to appear.

repo_name

The name of the repo. If must be set if repo_url is set.

repo_type

Must be one of github, gitlab or bitbucket.

base_url

Specify a base_url used to generate sitemap.xml links. If not specified, then no sitemap will be built.

globaltoc_depth

The maximum depth of the global TOC; set it to -1 to allow unlimited depth.

globaltoc_collapse

If true, TOC entries that are not ancestors of the current page are collapsed.

globaltoc_includehidden

If true, the global TOC tree will also contain hidden entries.

theme_color

The theme color for mobile browsers. Hex Color without the leading #.

color_primary

Primary color. Options are red, pink, purple, deep-purple, indigo, blue, light-blue, cyan, teal, green, light-green, lime, yellow, amber, orange, deep-orange, brown, grey, blue-grey, and white.

color_accent

Accent color. Options are red, pink, purple, deep-purple, indigo, blue, light-blue, cyan, teal, green, light-green, lime, yellow, amber, orange, and deep-orange.

html_minify

Minify pages after creation using htmlmin.

html_prettify

Prettify pages, usually only for debugging.

css_minify

Minify css files found in the output directory.

logo_icon

Set the logo icon. Should be a pre-escaped html string that indicates a unicode point, e.g., '&#xe869' which is used on this site.

master_doc

Include the master document at the top of the page in the breadcrumb bar. You must also set this to true if you want to override the rootrellink block, in which case the content of the overridden block will appear

nav_links

A list of dictionaries where each has three keys:

href : The URL or pagename (str)
title : The title to appear (str)
internal : Flag indicating to use pathto to find the page. Set to False for external content. (bool)

heroes

A dict[str,str] where the key is a pagename and the value is the text to display in the page’s hero location.

version_dropdown

A flag indicating whether the version drop down should be included. You must supply a JSON file to use this feature.

version_dropdown_text

The text in the version dropdown button

version_json

The location of the JSON file that contains the version information. The default assumes there is a file versions.json located in the root of the site.

version_info

A dictionary used to populate the version dropdown. If this variable is provided, the static dropdown is used and any JavaScript information is ignored.

table_classes

A list of classes to not strip from tables. All other classes are stripped, and the default table has no class attribute. Custom table classes need to provide the full style for the table.

1.2. Sidebars ¶

You must set html_sidebars in order for the side bar to appear. There are four in the complete set.

         html_sidebars = {
    "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
}

        

You can exclude any to hide a specific sidebar. For example, if this is changed to

         html_sidebars = {
    "**": ["globaltoc.html"]
}

        

then only the global ToC would appear on all pages ( ** is a glob pattern).

1.3. Customizing the layout ¶

You can customize the theme by overriding Jinja template blocks. For example, 〈layout.html〉 contains several blocks that can be overridden or extended.

Place a 〈layout.html〉 file in your project’s 〈/_templates〉 directory.

         mkdir source/_templates
touch source/_templates/layout.html

Then, configure your 〈conf.py〉:

         templates_path = ['_templates']

        

Finally, edit your override file source/_templates/layout.html :

         {# Import the theme's layout. #}
{% extends '!layout.html' %}

{%- block extrahead %}
{# Add custom things to the head HTML tag #}
{# Call the parent block #}
{{ super() }}
{%- endblock %}

        

1.4. New Blocks ¶

The theme has a small number of new blocks to simplify some types of customization:

footerrel: Previous and next in the footer.
font: The default font inline CSS and the class to the google API. Use this block when changing the font.
fonticon: Block that contains the icon font. Use this to add additional icon fonts (e.g., FontAwesome ). You should probably call {{ super() }} at the end of the block to include the default icon font as well.

A version dropdown is available that lets you store multiple versions in a single site. The standard structure of the site, relative to the base is usually:

         /
/devel
/v1.0.0
/v1.1.0
/v1.1.1
/v1.2.0

        

To use the version dropdown, you must set version_dropdown to True in the sites configuration.

There are two approaches, one which stores the version information in a JavaScript file and one which uses a dictionary in the configuration.

1.5.1. Using a Javascript File ¶

The data used is read via javascript from a file. The basic structure of the file is a dictionary of the form [label, path].

This dictionary tells the dropdown that the release version is in the root of the site, the other versions are archived under their version number, and the development version is located in /devel.

참고

The advantage of this approach is that you can separate version information from the rendered documentation. This makes is easy to change the version dropdown in _older_ versions of the documentation to reflect additional versions that are released later. Changing the Javascript file changes the version dropdown content in all versions. This approach is used in statsmodels .

1.5.2. Using `conf.py` ¶

경고

This method has precedence over the JavaScript approach. If version_info is not empty in a site’s html_theme_options , then the static approach is used.

The alternative uses a dictionary where the key is the title and the value is the target. The dictionary is part of the size configuration’s html_theme_options .

The dictionary structure is nearly identical. Here you can use relative paths like in the JavaScript version. You can also use absolute paths.

참고

This approach is easier if you only want to have a fixed set of documentation, e.g., stable and devel.