Notebooks for reproducing all figures and analysis in the Transcriptomic responses to endurance exercise training in rats preprint.
All analysis notebooks, saved as .ipynb's in analysis scripts, can be run from Google Colab. Colab links are included in every notebook.
All saved/processed data used for analysis is streamed to the notebooks from CaltechData.
- Initial RNA Analysis
- Initial clustering and filtering of input matrix
- Generates Figure 1b
- Label Correction and Reanalysis
- Rescues mislabeled samples then re-filters/clusters the samples
- scVI Batch Correction
- Generates Supplemental Figures 3a-d
- Rat Individual Overview
- Visualizes distribution of samples across -omics and individuals
- Generates Figure 1a and Supplemental Figure 1
- Linear Regression RNA
- Concatenates tissue samples by individual rat then runs linear regression
- Generates Figure 1d and Supplemental Figures 2 and 6
- Linear Regression Physiological
- Concatenates tissue samples by individual rat then runs linear regression
- Generates Supplemental Figures 8a, 8b, and 9
- Partial Correlation Analysis
- Concatenates tissue samples by individual rat then runs linear regression
- Linear Regression scVI
- Concatenates tissue samples by individual rat then runs linear regression
- Generates Supplemental Figure 7
- Rat Omic Loading
- Loads -omic data and adds metadata
- Linear Regression Omic
- Concatenates tissue samples by individual rat then runs linear regression
- Generates Supplemental Figures 4, 10a, and 10b
- ATAC and METHYL Analysis
- Generates PCA plots of ATAC and METHYL data
- Generates Supplemental Figures 5a, 5b, and 11
- DEseq
- Differential gene expression analysis
- Generates Figures 2a-i
- Virus Filtering
- Virus Filtering to remove known contaminates
- Virus Correlation Over Time
- Correlates virus quantity over time
- Generates Figure 3a
- Virus DEseq
- Differential virus expression analysis
- Generates Figures 3b-e
- Virus BLAST
- BLAST of raw virus reads
- Generates Supplemental Figure 12