Afterglow manuscript reproducibility archive

Companion reproducibility archive for the manuscript "Afterglow: an R package for half-life-aware analysis of standard RNA-seq responses". The archive contains manuscript-specific analysis scripts, input manifests, derived result summaries, generated analysis figures, session-information files and the package source tarball used as the software version anchor. Manuscript TeX/PDF source files and separate manuscript figure folders are not included in this archive. Large raw GEO files and the full TTDB CSV snapshot are not redistributed; their public sources and expected filenames are listed in the included input manifest.