This repository contains the data and code to reproduce the results presented in the paper Total replacement of fish meal with black soldier fly (Hermetia illucens) larvae meal does not compromise the gut health of Atlantic salmon (Salmo salar).
To rerun the analyses online, simply click on the Binder badge. Note that this's still under testing and may fail.
To rerun the analyses locally, download this repository as a zipped file. After decompression, open the R project file (AqFl2_GutHealth.Rproj) in the RStudio and run the R codes directly from the project root directory. Versions of R packages for each anaylsis can be found in the session information (*_sessionInfo.txt) under the same folder of R codes.
Below is an overview of the file organization descending to level-3 directories.
root
├── analysis
│ ├── code
│ │ ├── histology.R
│ │ ├── histology_sessionInfo.txt
│ │ ├── organosomatic_index.R
│ │ ├── organosomatic_index_sessionInfo.txt
│ │ ├── qPCR_ref_DI.R
│ │ ├── qPCR_ref_DI_sessionInfo.txt
│ │ ├── qPCR_ref_PI.R
│ │ ├── qPCR_ref_PI_sessionInfo.txt
│ │ ├── qPCR_target_DI.R
│ │ ├── qPCR_target_DI_sessionInfo.txt
│ │ ├── qPCR_target_PI.R
│ │ └── qPCR_target_PI_sessionInfo.txt
│ ├── exploratory_analysis
│ │ ├── histology_histogram.pdf
│ │ ├── OSI_boxPlot.pdf
│ │ ├── OSI_violin.pdf
│ │ ├── qPCR_ref_DI_barPlot.pdf
│ │ ├── qPCR_ref_DI_boxPlot.pdf
│ │ ├── qPCR_ref_DI_pointDiagram.pdf
│ │ ├── qPCR_ref_PI_barPlot.pdf
│ │ ├── qPCR_ref_PI_boxPlot.pdf
│ │ ├── qPCR_ref_PI_pointDiagram.pdf
│ │ ├── qPCR_target_DI_boxPlot.pdf
│ │ ├── qPCR_target_DI_heatmap.pdf
│ │ ├── qPCR_target_DI_violin.pdf
│ │ ├── qPCR_target_PI_boxPlot.pdf
│ │ ├── qPCR_target_PI_heatmap.pdf
│ │ └── qPCR_target_PI_violin.pdf
│ └── model_diagnostics
│ ├── OSI_LMMs_residual.pdf
│ ├── OSI_welch-t_qqplot.pdf
│ ├── qPCR_DI_LMMs_residual.pdf
│ ├── qPCR_DI_welch-t_qqplot.pdf
│ ├── qPCR_PI_LMMs_residual.pdf
│ └── qPCR_PI_welch-t_qqplot.pdf
├── AqFl2_GutHealth.Rproj
├── data
│ ├── clean_data
│ │ ├── AqFl2_qPCR_ref_DI.csv
│ │ ├── AqFl2_qPCR_ref_PI.csv
│ │ ├── AqFl2_qPCR_Target_DI.csv
│ │ ├── AqFl2_qPCR_Target_PI.csv
│ │ └── Interplate_calibration.xlsx
│ ├── raw_data
│ │ ├── AqFl2_histology.csv
│ │ ├── AqFl2_LightCycler_files
│ │ └── AqFl2_organosomatic_index.csv
│ └── README.md
├── LICENSE
├── README.md
└── results
├── figures
│ ├── Figure 1.tiff
│ ├── Figure 2.tiff
│ ├── Figure 3.tiff
│ └── Figure 4.tiff
└── reference_gene_ranks
├── ref_gene_rank_DI.pdf
└── ref_gene_rank_PI.pdf