Reproduction package for: Long Read RNA Sequencing in Primary Lung Cell Types Reveals Principles of Nonsense-Mediated Decay
Year: 2026
Type: software
Abstract: Analysis code that reproduces the figures and reported numbers of Leshem et al., Long Read RNA Sequencing in Primary Lung Cell Types Reveals Principles of Nonsense-Mediated Decay. Code only. The data this code runs on are archived separately as the source-data record (DOI 10.5281/zenodo.21544336), which also carries the container image nmd_1.3.sif. That image is a corrected rebuild from the same pinned lockfile as the image the analyses ran under, rather than a byte-identical copy of it; the source-data record's own README explains the difference. Raw sequencing reads are in NCBI GEO under GSE329233 and are not required. Start with README.md, which gives the reading order. ENVIRONMENT.md covers the container and how to run it; REPRODUCTION.md gives the ordered run; RESULTS_INDEX.md maps reported numbers to the scripts that produce them.
Authors: Leshem, Yul, Kasai, Yoshiyuki, Eskandar, Masih, Thakur, Sanika M., Santos Cabrera, Jose, Runyan, Matthew, Paul, Ayan, Ziniti, John, Boueiz, Adel, Saferali, Aabida, De Marzio, Margherita, Dy, Jennifer, Laederach, Alain, Tata, Aleksandra, Tata, Purushothama Rao, Randell, Scott H., Castaldi, Peter J.
Language: English
Topic: RNA Research and Splicing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7202399997