Public repository for Vassar Ribosome Lab transcriptomics/translatomics utilities. Includes R, Python, and SLURM utilities for alignment, quantification, TE change calculation with DESeq, thermodynamic structure prediction, and downstream analysis.
R utilities and examples for differential expression analysis with DESeq2.
SLURM and Python utilities and examples for long-read sequencing analysis.
R scripts for statistical modeling of differential expression data.
SLURM and python utilities and examples for mRNA secondary structure prediction (with RNAplfold from ViennaRNA) and subsequent analysis.
Miscillaneous R and Python analyses.
- Hopper-Junior-Manual.pdf: Document explaining how to use Hopper, Vassar's high-performance computing cluster. Hopper is essential for processes that require a lot of compute and storage, such as the Epi2me transcriptomes workflow, or our custom long-read workflows.