This repository contains the scripts used for the paper 'A proteogenomic atlas of the human neural retina' by Riepe et al. (2024).
Raw PacBio Iso-Seq data are available at the European Genome-phenome Archive (EGA) under accession number EGAD50000000101. The mass-spectromety proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD045187. Intermediate files generated during the analysis and reference files can be downloaded from Zenodo:
- reference data:
- intermediate analysis files:
The processed data is available as UCSC genome browser track (https://genome-euro.ucsc.edu/s/tabeariepe/retina_atlas).
- Data can be used to store the downloaded data from Zenodo to rerun the scripts
- Figures and Tables contains scripts used to create the figures and tables
- Proteomics contains all scripts used for the proteogenomic analysis
- Transcriptomics contains all scripts for the Iso-Seq analysis
- Retina specific exons describes how we looked for previous identified retina-specific exons in our PacBio dataset
- Scripts contains small scripts and functions used for the analysis