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video tutorial fixed
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@cparsania
cparsania committed Feb 23, 2023
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6 changes: 5 additions & 1 deletion inst/app/rmd_and_html/citations.Rmd
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Expand Up @@ -21,7 +21,11 @@ knitr::opts_chunk$set(
#library(FungiExpresZ)
```

## List of articles citing FungiExpresZ
# Cite FungiExpresZ

- Chirag Parsania, Ruiwen Chen, Pooja Sethiya, Zhengqiang Miao, Liguo Dong, Koon Ho Wong, FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery, *Briefings in Bioinformatics*, 2023;bbad051, <https://doi.org/10.1093/bib/bbad051>

# List of articles citing FungiExpresZ

## 2022

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111 changes: 90 additions & 21 deletions inst/app/rmd_and_html/citations.html
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11 changes: 11 additions & 0 deletions inst/app/rmd_and_html/rsconnect/documents/tutorial.Rmd/rpubs.com/rpubs/Document.dcf
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name: Document
title:
username:
account: rpubs
server: rpubs.com
hostUrl: rpubs.com
appId: https://api.rpubs.com/api/v1/document/1006717/36ac2443035d45b298d1c29608527670
bundleId: https://api.rpubs.com/api/v1/document/1006717/36ac2443035d45b298d1c29608527670
url: http://rpubs.com/publish/claim/1006717/3e7363cbc726447da80e7228d86918f7
when: 1677151205.738
lastSyncTime: 1677151205.73802
130 changes: 89 additions & 41 deletions inst/app/rmd_and_html/tutorial.Rmd
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Expand Up @@ -31,138 +31,186 @@ text-align: justify}

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
frame_width = 800
frame_height = 500
```

# How to use SRA data

`r params$app_name` contains normalised gene expression values for more than `r params$n_sra_data` NCBI SRA data. In this video, we show that how to select any of these data for downstream analysis and visualization purpose.

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/B4hwnLijEB8" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "B4hwnLijEB8",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

# How to upload user data

Along with NCBI SRA data, user can also upload his own gene expression matrix for data analysis and visualisation. In this video, we show that how user can upload his own data on `r params$app_name` for further analysis and visualizations.

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/4INn1AhEoO4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
vembedr::embed_youtube(id = "4INn1AhEoO4",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
</iframe>
```

# How to upload sample groups and gene groups

To address the complexity of gene expression data, `r params$app_name` allows user to integrate gene group and sample group information. In this video, we show that how to upload gene groups and sample groups on the `r params$app_name` to further integrate them in the visualizations.

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/H2gdBGUP9XY" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "H2gdBGUP9XY",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

# How to use predefined NCBI BioProjects as sample groups

[NCBI BioProject](https://www.ncbi.nlm.nih.gov/bioproject){target="_blank"} groups single initiative, originating from a single organization or from a consortium SRA runs under single BioProject ID. Diverse data types generated under single study can be find under single BioProject ID. `r params$app_name` allows user to use BioProject ID as sample groups for selected SRA data. The group information can be used across several plots for comparisons between multiple groups. In this video, we show that how to use given NCBI BioProject IDs as a sample groups.

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/8OeorXH6mUk" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "8OeorXH6mUk",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

# How to merge user data with SRA data

Integrated analysis of user gene expression data and public SRA data is one of the ways to build data driven hypothesis. `r params$app_name` allows user seamlessly integrate his/her own gene expression data with selected SRA data. In this video, we show that how to integrate user gene expression data with selected SRA data.

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/tO-78TTX93M" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "tO-78TTX93M",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

# Generate plots

`r params$app_name` can generate `r params$n_plots` different exploratory plots and `r params$n_go_plots` different GO plots. Below several videos show that how to generate different exploratory plots once data uploaded on the `r params$app_name`.

## Scatter plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/Z4UVAnI6CJA" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "Z4UVAnI6CJA",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Multi-scatter plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/d_TDT46m_v8" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "d_TDT46m_v8",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## CorrHeat box

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/G8EEwA1PKR0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "G8EEwA1PKR0",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Density plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/RPkpV4vXJU0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "RPkpV4vXJU0",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Histogram

<iframe width="1000" height="1000" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/O_YNFr0Tl5Y" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "O_YNFr0Tl5Y",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Joy plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/_2W1sutAkZE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "_2W1sutAkZE",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Box plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/Qic-ukmEUNQ" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "Qic-ukmEUNQ",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Violin plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/Rta2Nz1DKCw" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "Rta2Nz1DKCw",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## bar plot
## Bar plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/8ekS2Y1oRZs" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "8ekS2Y1oRZs",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## PCA

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/MEeaJKI5wLY" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "MEeaJKI5wLY",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Line plot

<iframe width="1000" height="700" src="https://www.youtube.com/embed/C24WL8rtZIU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "C24WL8rtZIU",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## Heatmap

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/yZH1ioPjmR0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "yZH1ioPjmR0",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

# Gene Ontology (GO) analysis and gene annotations

Once the genes of similar expression pattern have been found, next step is to perform GO analysis to look for biological insights from gene expression data. `r params$app_name` allows user to select genes and gene cluster(s) of similar expression pattern directly from scatter plot and, line plot and heatmap for GO analysis and gene annotations. In these videos, we show that how to perfom GO analysis from scatter plot and heatmap on `r params$app_name`.

## GO analysis from scatter plot

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/KTIgFVhKPBY" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>
vembedr::embed_youtube(id = "KTIgFVhKPBY",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```

## GO analysis from heatmap

<iframe width="1000" height="700" style="border: 2px solid #000000;" src="https://www.youtube.com/embed/Plsat-crwE0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
```{r, include=TRUE, echo=FALSE}
</iframe>

## GO analysis from scatter plot
vembedr::embed_youtube("Plsat-crwE0",
width = frame_width, height = frame_height,frameborder = "2px solid #000000",allowfullscreen = TRUE)
```
258 changes: 185 additions & 73 deletions inst/app/rmd_and_html/tutorial.html
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6 changes: 3 additions & 3 deletions rsconnect/shinyapps.io/cparsania/FungiExpresZ.dcf
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Expand Up @@ -5,10 +5,10 @@ account: cparsania
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 624687
bundleId: 6425274
bundleId: 6878779
url: https://cparsania.shinyapps.io/FungiExpresZ/
when: 1666317530.51392
lastSyncTime: 1666317530.51396
when: 1677155188.59316
lastSyncTime: 1677155188.59318
asMultiple: FALSE
asStatic: FALSE
ignoredFiles: _Dockerfile|.Rprofile|Dockerfile

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