This repository contains R markdown files and input datasets for the transcriptomic analysis of Rhodoluna lacicola and Aurantimicrobium sp. strain MWH-Mo1 time-series RNA-seq data.
Input data files are included in this repository. Running these scripts requires R studio.
There are three .Rmd files for the bioinformatic analysis of R.lacicola and Aurantimiccrobium sp. strain MWH-Mo1 light/dark cycling RNA-Seq data:
- timeseries_transcriptome_analysis.Rmd
This code is for the DSEQ2 and hierarchical clustering analyses and related plots.
The input files for this analysis are:
1a. ta8_raw_counts_formatted.txt
1b. ta8_rc_formated_col_conditions.txt
1c. raw_count_formated.txt
1d. raw_count_formated_col_conditions.txt
- GO_Term_Distribution_Plot.Rmd
This code is for the GO-slim term distribution analysis and related plots.
The input files for this analysis are:
2a. Ta8_go_slim_count.txt
2b. Mo1_go_slim_count.txt
- Fisher_Test_Analysis.Rmd
This code is for the odds ratio calculation and related plots of the merged hierarchically clustered gene groups.
The input files are:
3a. Ta8_Macro_Groups_Fischer_Test_Data.csv
3b. Mo1_Macro_Groups_Fischer_Test_Data.csv