BioinfOMICS/LipidTrend-source: LipidTrend-source v1.0.1

All analyses regenerated with LipidTrend 1.3.1, under a fixed random seed and a fully locked computational environment. Repository releases are numbered after the LipidTrend version whose results they contain. Analysis scripts RNGkind() is pinned and set.seed(1234) is called immediately before every analyzeLipidRegion() call, so every figure and table is reproducible. The previous scripts set no seed. Paths are now relative to the repository root, replacing the ~/data/... template that had to be edited by hand. regionalTestFC() tables are written alongside each smoothing result: the region-level paired t-test and fold-change introduced in LipidTrend 1.3.1. Fixed four references to an undefined cor.res in scripts/HCC/tsne1_tsne0/TG/coordinate_correlation.R. Computational environment renv.lock now records the complete environment: 122 packages, R 4.5.2, Bioconductor 3.22. The previous lockfile listed only renv itself. LipidTrend 1.3.1 ships as a source tarball in renv/cellar/, so renv::restore() installs exactly the version used here. renv/library/ is no longer tracked. It holds platform-specific binaries that cannot be restored on another machine; each machine now builds its own library from the lockfile. New in this repository run_all.R runs all 27 analysis scripts, each in its own R process, and writes a status table to logs/run_summary.tsv. REPRODUCIBILITY.md documents the environment, the changes above, and the verification performed. docs/data_checksums.txt lists SHA-256 checksums for the 26 input files. Reproducing Start R in the repository root, then: install.packages("renv") renv::restore() source("run_all.R")