This repository stores the scripts used to perform the following tasks:
- Exploratory analyses for proteomics datasets analyzed by OneOmics and Spectronaut;
- Differential expression analysis for RNA-Seq data;
- Plots.
Brief description of each file stored in scripts folder:
- 0_loadingLibs.R: Loads all libraries required to run the entire analysis.
- 1_locusTagDict.R: Load a dictionary of locus_tags from halo_nr_tx. This is required to integrate the proteomics dataset to the gene expression dataset. To improve the number of matched entries, we use an approach based in Reciprocal Best BLAST-Hit.
- 2_parseOneOmicsResults.R: Parse and filter proteomics results; Plot and save the volcano plot and the heat map for the OneOmics dataset.
- 3_PlotPCAOneOmics.R: Parse PCA data generated by OneOmics and plot/save the figure.
- 4_parseSpectronautResults.R: Read and parse abundance data provided by Spectronaut; Generate and save the heat map for this dataset.
- 5_PlotPCASpectronaut.R: Wrangle Spectronaut dataset and run PCA followed by its plot.
- 6_RNADEanalysis.R: Read kallisto count data generated by runKallisto pipeline and perform differential expression analysis.
- 7_parseAndGenScatters.R: Parse protein and mRNA levels and relative changes and generate scatter plots between those two variables.
- 8_additionalAnalyses.R: Additional sanity checks and a plot for the comparison of mRNA levels of detected and undetected proteins.
This set of scripts is powered by RStudio, tidyverse, and Bioconductor.