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index.Rmd
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---
title: '**BioPAN Tutorial**'
subtitle: This document was prepared on `r format(Sys.Date())`.
output:
html_document:
theme: cerulean
highlight: pygments
toc: yes
toc_depth: 2
toc_float:
collapsed: true
smooth_scroll: true
number_sections: no
df_print: kable
code_folding: hide
code_download: yes
self_contained: false
lib_dir: "docs/rmarkdown_libs"
rmarkdown::html_vignette:
toc: yes
toc_depth: 2
editor_options:
chunk_output_type: console
bibliography: utils/bibliography.bib
csl: utils/f1000research.csl
---
<!--
!!!! IMPORTANT: run `source("utils/render.R")` to publish instead of clicking on 'Knit'
# See https://yihui.org/knitr/options/
-->
```{r setup, warning=FALSE, message=TRUE, include=FALSE}
# Set up the environment
# Options relative to figure size
# 1.618 is the golden ratio
figheight <- 4
figwidth <- 4 * 1.618
# General options
options(knitr.kable.NA = "",
nsmall = 3,
tidyverse.quiet = TRUE)
# Chunk options (see https://yihui.org/knitr/options/#chunk_options)
knitr::opts_chunk$set(
comment = ">", # The prefix to be added before each line of the text output.
dpi = 600,
fig.path = "figures/",
fig.height = figheight,
fig.width = figwidth,
fig.align = "center",
# See https://community.rstudio.com/t/centering-images-in-blogdown-post/20962
# to learn how to center images
# See https://bookdown.org/yihui/rmarkdown-cookbook/opts-tidy.html
# See https://www.zotero.org/styles for citation style respository
tidy='styler',
tidy.opts=list(strict=TRUE)
)
fast <- FALSE # Make this false to skip the chunks
```
# Agenda
This document helps to explain how the number displayed in the BioPAN software are calculated using a small dataset as an example. The source code of this document can be found in this [GitHub respository](https://github.com/JauntyJJS/BioPAN_Tutorial)
# About BioPAN
[BioPAN](https://f1000research.com/articles/10-4) [@BIOPAN] is a tool found in [LIPID MAPS](https://lipidmaps.org/biopan) designed to automate biosynthetic pathway analysis of lipids.
![](figures/giz061_ActivePCtoPStoPE_pathway.PNG)
Below is a [YouTube video](https://www.youtube.com/watch?v=3OrjRzbCB04) on how to use BioPAN.
<p align="center">
<iframe width="560" height="315" src="https://www.youtube.com/embed/3OrjRzbCB04" frameborder="0" allowfullscreen></iframe>
</p>
The [documentation](https://www.lipidmaps.org/biopan/doc/step3_build.html) of BioPAN provides a technical explanation of how the pathway scores are calculated.
![](figures/giz061_BioPAN_techincal_details.PNG)
More information can be found in this [paper](https://doi.org/10.1016/j.copbio.2016.10.003) [@NGUYEN201796]
# Packages
```{r warning=FALSE, message=FALSE, results='asis'}
library(styler)
library(dplyr)
library(magrittr)
library(report)
summary(report::report(sessionInfo()))
```
# Data {.tabset}
```{r child=if (fast == FALSE) '1_about_data.Rmd'}
```
# BioPAN on Lipid Species {.tabset}
```{r child=if (fast == FALSE) '2_BioPAN_species_case.Rmd'}
```
# BioPAN on Lipid Class {.tabset}
```{r child=if (fast == FALSE) '3_BioPAN_class_case.Rmd'}
```
# Rmarkdown Template
This Rmarkdown template is created by the [Reality Bending Lab](https://realitybending.github.io/). The template can be download from the lab's [github](https://github.com/RealityBending/TemplateResults) repository. For more information about the motivation behind creating this template, check out [Dr. Dominique Makowski's blog post](https://dominiquemakowski.github.io/post/2021-02-10-template_results/)
# Package References
```{r warning=FALSE, message=TRUE, results='asis'}
report::cite_packages(sessionInfo())
```
# References