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vincerubinetti authored and dhimmel committed Mar 13, 2019
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  2. +1 −1 content/citation-tags.tsv
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## Manubot Rootstock Information
This manuscript is a template (aka "rootstock") for [Manubot]( "Manubot"), a tool for writing scholarly manuscripts.
Use this template as a starting point for your manuscript.

**Note: Manubot instances should delete this file.**
The rest of this document is a full list of formatting elements/features supported by Manubot.
Compare the input (`.md` files in the `/content` directory) to the output you see below.

The Manubot is a system for automating scholarly publishing.
Content is written in [Pandoc Markdown]( source files.
See [``]( for more information on how to use the Manubot.
## Basic formatting

The Manubot project began with the [Deep Review](, where it was used to compose a highly-collaborative review article [@doi:10.1098/rsif.2017.0387].
Another example manuscript that was created with Manubot is:
**Bold** __text__

+ The Sci-Hub Coverage Study ([GitHub](, [HTML manuscript]( [@doi:10.7554/eLife.32822]
[Semi-bold text]{.semibold}

If you notice a problem with Manubot, it's best to submit an upstream fix to the appropriate repository:
[`greenelab/manubot-rootstock`]( for the git repository stub or [`greenelab/manubot`]( for the Python package.
[Centered text]{.center}

[Right-aligned text]{.right}

*Italic* _text_

Combined *italics and __bold__*


1. Ordered list item
2. Ordered list item
a. Sub-item
b. Sub-item
i. Sub-sub-item
3. Ordered list item
a. Sub-item

- List item
- List item
- List item



[unicode superscripts](⁰¹²³⁴⁵⁶⁷⁸⁹

[unicode subscripts](₀₁₂₃₄₅₆₇₈₉

A long paragraph of text.
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.
Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Putting each sentence on its own line has numerous benefits with regard to [editing]( and [version control](

Line break without starting a new paragraph by putting
two spaces at end of line.

## Document organization

Document section headings:

# Heading 1

## Heading 2

### Heading 3

#### Heading 4

### A heading centered on its own printed page{.center .page_center}

<!-- an arbitrary comment. visible in input, but not visible in output. -->

Horizontal rule:


`Heading 1`'s are recommended to be reserved for the title of the manuscript.

`Heading 2`'s are recommended for broad sections such as *Abstract*, *Methods*, *Conclusion*, etc.

`Heading 3`'s and `Heading 4`'s are recommended for sub-sections.

## Links

Bare URL link: <>

[Link with text](

[Link with hover text]( "Manubot Homepage")

[Link by reference][manubot homepage]

[Manubot Homepage]:

## Citations

Citation by DOI [@doi:10.7554/eLife.32822].

Citation by PubMed Central ID [@pmcid:PMC6103790].

Citation by PubMed ID [@pmid:30718888].

Citation by Wikidata ID [@wikidata:Q56458321].

Citation by ISBN [@isbn:9780262517638].

Citation by URL [@url:].

Citation by tag [@tag:deep-review].

Multiple citations can be put inside the same set of brackets [@doi:10.7554/eLife.32822; @tag:deep-review; @isbn:9780262517638].
Manubot plugins provide easier, more convenient visualization of and navigation between citations [@url:; @pmid:30718888; @pmcid:PMC6103790; @tag:deep-review].

## Referencing figures, tables, equations

Figure @fig:square-image

Figure @fig:wide-image

Figure @fig:tall-image

Figure @fig:vector-image

Table @tbl:bowling-scores

Equation @eq:regular-equation

Equation @eq:long-equation

## Quotes and code

> Quoted text

> Quoted block of text
> Two roads diverged in a wood, and I—
> I took the one less traveled by,
> And that has made all the difference.

Code `in the middle` of normal text, aka `inline code`.

Code block with Python syntax highlighting:

from manubot.cite.doi import expand_short_doi
def test_expand_short_doi():
doi = expand_short_doi("10/c3bp")
# a string too long to fit within page:
assert doi == "10.25313/2524-2695-2018-3-vliyanie-enhansera-copia-i-insulyatora-gypsy-na-sintez-ernk-modifikatsii-hromatina-i-svyazyvanie-insulyatornyh-belkov-vtransfetsirovannyh-geneticheskih-konstruktsiyah"

Code block with no syntax highlighting:

Exporting HTML manuscript
Exporting DOCX manuscript
Exporting PDF manuscript

## Figures

**A square image at actual size and with a bottom caption.**
Loaded from the latest version of image on GitHub.
]( "Square image"){#fig:square-image}

**An image too wide to fit within page at full size.**
Loaded from a specific (hashed) version of the image on GitHub.
]( "Wide image"){#fig:wide-image}

**A tall image with a specified height.**
Loaded from a specific (hashed) version of the image on GitHub.
]( "Tall image"){#fig:tall-image height=3in}

**A vector `.svg` image loaded from GitHub.**
The parameter `sanitize=true` is necessary to properly load SVGs hosted via GitHub URLs.
White background specified to serve as a backdrop for transparent sections of the image.
]( "Vector image"){#fig:vector-image height=2.5in .white}

## Tables

| *Bowling Scores* | Jane | John | Alice | Bob |
| Game 1 | 150 | 187 | 210 | 105 |
| Game 2 | 98 | 202 | 197 | 102 |
| Game 3 | 123 | 180 | 238 | 134 |

Table: A table with a top caption and specified relative column widths.

| | Digits 1-33 | Digits 34-66 | Digits 67-99 | Ref. |
| pi | 3.14159265358979323846264338327950 | 288419716939937510582097494459230 | 781640628620899862803482534211706 | [``]( |
| e | 2.71828182845904523536028747135266 | 249775724709369995957496696762772 | 407663035354759457138217852516642 | [``]( |

Table: A table too wide to fit within page.

## Equations

A LaTeX equation:

$$\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}$$ {#eq:regular-equation}

An equation too long to fit within page:

$$x = a + b + c + d + e + f + g + h + i + j + k + l + m + n + o + p + q + r + s + t + u + v + w + x + y + z + 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9$$ {#eq:long-equation}

## Special

<i class="fas fa-exclamation-triangle"></i> [WARNING]{.semibold} _The following features are only supported and intended for `.html` and `.pdf` exports._
_Journals are not likely to support them, and they may not display correctly when converted to other formats such as `.docx`._

[Link styled as a button]( "Manubot Homepage"){.button}

Available background colors for text, images, code, banners, etc:


Using the [Font Awesome]( icon set:

<!-- include the Font Awesome library, per: -->
<link rel="stylesheet" href="">

<i class="fas fa-check"></i> <i class="fas fa-question"></i> <i class="fas fa-star"></i> <i class="fas fa-bell"></i> <i class="fas fa-times-circle"></i> <i class="fas fa-ellipsis-h"></i>

<i class="fas fa-scroll fa-lg"></i> **Light Grey Banner**<br>
useful for *general information* - [](
]{.banner .lightgrey}

<i class="fas fa-info-circle fa-lg"></i> **Blue Banner**<br>
useful for *important information* - [](
]{.banner .lightblue}

<i class="fas fa-ban fa-lg"></i> **Light Red Banner**<br>
useful for *warnings* - [](
]{.banner .lightred}
@@ -1,2 +1,2 @@
tag citation
deep_review doi:10.1101/142760
deep-review doi:10.1098/rsif.2017.0387
@@ -1,5 +1,5 @@
title: "Manubot Rootstock: Manuscript Title"
title: "Manuscript Title"
- markdown
- publishing

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