Yomics

Overview

Analysis and figure-generation code for a multi-omic study of the yeast translational response to acute glucose starvation. It jointly measures transcript abundance, degradation, poly(A) tail length, and three RNA modifications from native molecules, and fits a penalised mixture model that resolves distinct regulatory clusters.

Linux · macOS · Windows

Quick start

git clone https://github.com/Arnaroo/Yomics.git
cd Yomics/
# see README for the R and Python package requirements

What it is

Yomics is the analysis and figure-generation code behind a multi-omic study of the yeast translational response to acute glucose starvation in Saccharomyces cerevisiae, comparing non-starved and 10-minute starved conditions. It extends the eTCP-seq and Stochastic Translation Efficiency framework of Horvath et al. (2024, Nucleic Acids Research) with direct RNA sequencing of polysome-fractionated transcripts, jointly measuring transcript abundance, degradation, poly(A) tail length, and the m5C, m6A and pseudouridine modifications from native molecules.

Method

A lasso-penalised mixture-of-regressions model (flexmix with glmnet, k equal to 5) fit on 29 candidate features across 5,033 transcripts identifies five regulatory clusters with distinct translational responses to starvation. Random seeds are fixed throughout for reproducibility.

Repository layout

• PreProcessing: shell pipelines for degradation quantification (INDEGRA), RNA modification calling, and poly(A) tail length estimation from raw sequencing data.
• Entropy: k-mer entropy and nucleotide composition analyses of UTRs and CDS.
• Multi_Omic_Integration: R scripts building the integrated per-transcript feature table, fitting the mixture model, and extracting cluster assignments, feature importances and GO enrichment.
• Figures: one folder per main and supplementary figure, with the R and Python scripts that generate it.