-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.Rmd
87 lines (57 loc) · 4.5 KB
/
index.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
---
title: "UCSCXenaShiny v2 Book"
author: "Shensuo Li, Shixiang Wang"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
# url: your book url like https://bookdown.org/yihui/bookdown
# cover-image: path to the social sharing image like images/cover.jpg
description: |
This is a minimal example of using the bookdown package to write a book.
The HTML output format for this example is bookdown::gitbook,
set in the _output.yml file.
link-citations: yes
github-repo: rstudio/bookdown-demo
---
# About {-}
**UCSCXenaShiny** is an R package for interactively exploring UCSC Xena datasets. It is mainly designed to provide a web app (built on the top of [`{shiny}`](https://shiny.rstudio.com/) framework and [`{UCSCXenaTools}`](https://github.com/ropensci/UCSCXenaTools/) package) for downloading, analyzing and visualizing datasets from [UCSC Xena](https://xenabrowser.net/datapages/). In the latest version, the application can support both general and personalized tumor molecular analysis with versatile functional modules and user-friendly interface layouts. Overall, our tool aims to make best use of public omics data from UCSC Xena and assist broad user community with precision oncology research.
```{r p0000_1, fig.align='center', echo = FALSE, out.width="100%"}
knitr::include_graphics('images/p0000_1.png')
```
Here, we have prepared the tutorial book to introduce the detailed usage of UCSCXenaShiny based on R Markdown and [bookdown](https://github.com/rstudio/bookdown). Firstly, we will start with the basic knowledge of UCSC Xena repository and its data hubs in **Chapter \@ref(intro)**. Then, the following chapters can be generally divided into two parts for the usage of R package and Shiny App:
#### Part Ⅰ {-}
- **Chapter \@ref(install)**：The ways to install UCSCXenaShiny package.
- **Chapter \@ref(build-in)**：Avalilable built-in datasets of package, e.g. clinical or survival data.
- **Chapter \@ref(data-query)**：The functions to query molecular data of TPC datasets.
- **Chapter \@ref(data-analysis)**：The functions to perform various analyses based on TPC datasets.
#### Part Ⅱ {-}
- **Chapter \@ref(visit)**：The ways to visit UCSCXenaShiny application.
- **Chapter \@ref(home)**：The intuitive widgets and quick exploration modules in homepage.
- **Chapter \@ref(repo)**：The query for all datasets of UCSC Xena repository.
- **Chapter \@ref(general-da)**：General analysis modules for any matrix datasets.
- **Chapter \@ref(custom-tpc)**：Custom analysis modules for TPC datasets.
- **Chapter \@ref(per-tpc-1)**：The key preprocesses of personalized TPC pipelines.
- **Chapter \@ref(per-tpc-2)**：The versatile analyses of personalized TPC pipelines.
- **Chapter \@ref(download)**：Two download modules for the custom data subset.
#### Part Ⅲ {-}
We have recorded a series of tutorial videos with step-by-step instructions:
**1. English version**
- Episode 1-4: https://www.youtube.com/watch?v=VnIlzcVB1Ow&list=PLN1jxcOQONG6pH8zvHr-qhI3MMtvluITf
```{r p0000_2, fig.align='center', echo = FALSE, out.width="90%"}
knitr::include_graphics('images/p0000_2.png')
```
**2. Chinese version**
- Episode 1: https://www.bilibili.com/video/BV1rT421k7Zv
- Episode 2: https://www.bilibili.com/video/BV1E14218779
- Episode 3: https://www.bilibili.com/video/BV141421t71g
- Episode 4: https://www.bilibili.com/video/BV1TZ421K7VH
___
Welcome to cite the following articles when **UCSCXenaShiny** has facilitated your study:
1. **UCSCXenaShiny** **v2** —
Li, S., Peng, Y., Chen, M. *et al.* Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny. *Commun Biol* **7**, 1200 (2024). https://doi.org/10.1038/s42003-024-06891-2
2. **UCSCXenaShiny** **v1** —
Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li, Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu, UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data, *Bioinformatics*, Volume 38, Issue 2, January 2022, Pages 527–529, https://doi.org/10.1093/bioinformatics/btab561
3. **UCSCXenaTools** —
Wang S and Liu X. The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
> If you have any question, please report to the [Github issues page](https://github.com/openbiox/UCSCXenaShiny/issues) or email to lishensuo@163.com