This project demonstrates another way of reporting statistical analysis results while independently reproducing DNA Zoo's summary table on the 17-year cicada genome assembly.
To reproduce DNA Zoo's summary table on the 17-year cicada and provide an accessible data analysis (DA) pipeline, documenting every data processing step.
The analysis pipeline consists of four main stages:
- Extract
- Transform
- Load
- Present
- Reproduces genome assembly statistics for the 17-year cicada
- Implements an ETL (Extract, Transform, Load) pipeline
- Uses Python, R, and Bash
- Provides step-by-step documentation of the data processing
First, have R and Python installed globally on your system.
In Rstudio:
Go to: File
Click New Project
Select Version Control
Paste this repo's code link
in R console:
install.packages("renv")renv::restore()renv::snapshot()Follow prompts to install R and Python packages during these steps where necessary. If doing this without an R console, you might be able to run that R code in R-code chunk(s) within the index.qmd file of the project.
01_Extract/: Data extraction scripts and raw data02_Transform/: Data transformation scripts and intermediate data03_Load/: Data loading scripts04_Present/: Data presentation scripts and final outputsindex.qmd: Quarto markdown document containing the analysis
All data used in this project is freely available from a public database hosted by DNA Zoo.
Eric Mossotti
This project is licensed under CC BY-SA.
This work builds upon the original research by DNA Zoo and the assembly_stats Python package developed by Mike Trizna.
For more details, please refer to the index.qmd file in this repository.