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README.Rmd
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---
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
```
# AtlaZ
## Description
AtlaZ is a toolkit designed for the analysis and visualization of zebrafish gene expression data across developmental stages and tissues. This package facilitates the integration of anatomical data, gene expression profiles, and ontological information, enabling researchers to explore the assortment of gene expression across developmental stages in zebrafish.
The package uses the E-ERAD-475 dataset available from the [Expression Atlas](https://www.ebi.ac.uk/gxa/experiments/E-ERAD-475/Downloads) which contains the expression values of all genes found in zebrafish across all developmental stages.
It was built as an R package, and was developed as a part of a course project for [BCB410H1: Applied Bioinformatics](https://artsci.calendar.utoronto.ca/course/bcb410h1) during the Fall 2023 semester at the University of Toronto. The development environment used was:
| Software | Version |
| --- | --- |
| R | 4.3.1 |
| Platform | arch64-apple-darwin20 (64-bit) |
| OS | macOS Sonoma 14.1.2 |
## Installation
To install the latest development version of AtlaZ, run the following code in R:
```r
install.packages("devtools")
library("devtools")
devtools::install_github("ashenafee/AtlaZ", build_vignettes = TRUE)
library("AtlaZ")
```
To run the Shiny app:
```r
runAtlaZ()
```
## Overview
To get an overview of AtlaZ in your R session, run the following code:
```r
ls("package:AtlaZ")
data(package = "AtlaZ")
browseVignettes("AtlaZ")
```
AtlaZ has one major class, `Gene`, which is used to store information about a gene. It has the following attributes:
| Attribute | Description |
| --- | --- |
| `geneSymbol` | The gene symbol of the gene. |
| `ensemblID` | The Ensembl ID of the gene. |
| `zfinID` | The ZFIN ID of the gene. |
| `anatomy` | An `AnatomyList` object containing information on the different possible areas where this gene is expressed. |
| `ontology` | An `OntologyList` object containing information on the different possible GO groups this gene falls into. |
The `AnatomyList` class stores many `Anatomy` objects which contain information on a specific area where a gene is expressed. In a similar fashion, the `OntologyList` class stores many `Ontology` objects which contain information on a specific GO group a gene falls into. These classes are a new addition as prior there was lots of wrangling with nested lists to get this information. By using these classes, it is much easier to access the information from one single `Gene` object.
**Data Visualization**
`plotGeneExpression` is a function that creates a line plot of gene expression values for a specific gene over different developmental stages. The line plot is an effective way to visualize how the expression of a particular gene changes across different stages of development. Each point on the line corresponds to a gene expression value at a particular developmental stage, and the line's progression shows the trend of these values over time. This can help researchers identify patterns or anomalies in gene expression, which can be critical in understanding gene function and its role in development.
`plotMultipleGeneExpression` does the same thing as `plotGeneExpression`, but for multiple genes. This is useful for comparing the expression of multiple genes across different developmental stages.
**Fetching from ZFIN**
`getZfinBackgroundInfo(zfinId: str)` is a function that fetches background information about a gene from ZFIN. This function was initially used to obtain the anatomical and ontological information, but `getGeneInfo()` is now favoured.
**Fetching from Ensembl**
`getGeneInfo(geneSymbols: str[])` is a function that fetches information on one or more genes from Ensembl. This function is used to populate the `Gene` object with information about the gene. This function is also used to populate the `AnatomyList` and `OntologyList` objects with information about the different areas where the gene is expressed and the different GO groups the gene falls into, respectively.
**Figure 1.** An overview of the AtlaZ workflow and how it works on a high level.
AtlaZ mainly uses the data from the [E-ERAD-475 dataset](https://www.ebi.ac.uk/gxa/experiments/E-ERAD-475/Downloads), and that's where most functionality is unlocked/tested.
If data is provided as input (i.e., it's from the user and **not** from ZFIN), it must be cleaned up and formatted first before it can be used by AtlaZ. This data must be formatted with the following headings: Gene ID, Gene Name, zygote, cleavage 2-cell, blastula 128-cell, blastula 1k-cell, blastula dome, gastrula 50%-epiboly, gastrula shield, gastrula 75%-epiboly, segmentation 1-4 somites, segmentation 14-19 somites, segmentation 20-25 somites, pharyngula prim-5, pharyngula prim-15, pharyngula prim-25, hatching long-pec, larval protruding mouth larval day 4, larval day 5.
A valid Ensembl identifier must be under `Gene ID` with a valid gene symbol under `Gene Name`. The rest of the columns can consist of numerical values as those represent expression values across each development stage.
## Contributions
My name is Ashenafee Mandefro, and I am the author of this package. I've worked with large databases similar to ZFIN in the past (i.e., GenBank, Ensembl) and I want to adapt my skills to a zebrafish context, given that fits into the context of my current thesis project at the [Lin Lab](https://lin.csb.utoronto.ca/). You can see more of my projects [here](https://github.com/ashenafee).
[Expression Atlas](https://www.ebi.ac.uk/gxa/home) is used as the primary data source in AtlaZ, with the primary dataset being [E-ERAD-475 dataset](https://www.ebi.ac.uk/gxa/experiments/E-ERAD-475/Downloads). Aside from Expression Atlas, more datasets are available for download from ZFIN from their website which is available [here](https://zfin.org/downloads). The data provided by ZFIN is licensed under the [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).
Generative AI was used to help with creating the initial documentation for each function. Specifically, GitHub Copilot was prompted with the contents of the function and an initial docstring, and it generated a final docstring that was then edited by the author. More information on GitHub Copilot is available [here](https://copilot.github.com/).
## References
Bradford, Y. M., Van Slyke, C. E., Ruzicka, L., Singer, A., Eagle, A., Fashena, D., Howe, D. G., Frazer, K., Martin, R., Paddock, H., Pich, C., Ramachandran, S., & Westerfield, M. (2022). Zebrafish information network, the knowledgebase for Danio rerio research. In V. Wood (Ed.), *Genetics* (Vol. 220, Issue 4). Oxford University Press (OUP). https://doi.org/10.1093/genetics/iyac016
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., & Huber, W. (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. *Bioinformatics*, Vol. 21, pp. 3439–3440.
Durinck, S., Spellman, P. T., Birney, E., & Huber, W. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. *Nature Protocols*, Vol. 4, pp. 1184–1191.
Sievert, C. (2021). Interactive Web-Based Data Visualization with R, Plotly, and Shiny. Chapman and Hall/CRC. https://plotly-r.com
Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis. Retrieved from https://ggplot2.tidyverse.org
Wickham, H., François, R., Henry, L., Müller, K., & Vaughan, D. (2023). dplyr: A Grammar of Data Manipulation. Retrieved from https://CRAN.R-project.org/package=dplyr
Wickham, H. (2023). httr: Tools for Working with URLs and HTTP. Retrieved from https://CRAN.R-project.org/package=httr
Wickham, H., Hester, J., & Bryan, J. (2023). readr: Read Rectangular Text Data. Retrieved from https://CRAN.R-project.org/package=readr
Wickham, H., Vaughan, D., & Girlich, M. (2023). tidyr: Tidy Messy Data. Retrieved from https://CRAN.R-project.org/package=tidyr
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. (2018, January). *Nucleic Acids Res*., Vol. 46, pp. D661–D667.
White, R. J., Collins, J. E., Sealy, I. M., Wali, N., Dooley, C. M., Digby, Z., Stemple, D. L., Murphy, D. N., Billis, K., Hourlier, T., Füllgrabe, A., Davis, M. P., Enright, A. J., & Busch-Nentwich, E. M. (2017). A high-resolution mRNA expression time course of embryonic development in zebrafish. In eLife (Vol. 6). *eLife Sciences Publications*, Ltd. https://doi.org/10.7554/elife.30860
## Acknowledgements
This package was developed as part of an assessment for 2023 BCB410H: Applied Bioinformat-
ics course at the University of Toronto, Toronto, CANADA. AtlaZ welcomes issues,
enhancement requests, and other contributions. To submit an issue, use the GitHub issues.