Release for final resubmission (2026/03/10) of PIBv1 manuscript titled "Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania". This release contains all relevant Nextflow pipelines including those used for both rounds of reviewer responses, and includes submodules for the analysis code and plotting scripts of sections performed by co-authors Daniela Tejada Martinez (@GenomeGaia), Stephen Rong (@stephenrong), Audrey Tjahjadi (@teriyakiaud), and Chang Liu (@Chg-Liu). See the README.md, PROCESSING.md, ANALYSIS.md, and PLOTS.md documents for a detailed description of all contained data processing, analyses, and plots.Files too large to be included in the Github repository have been added here as `PIBv1_manuscript_Plotting_inputs_20260304.zip` (for inputs to the scripts in the `Plotting` directory of the code repository) and `PIBv1_MPRA_analyses_bigfiles_20260304.zip` (for files too big to be included in Stephen Rong's PIBv1_MPRA_analyses repository/submodule). These archives have internal directory structure designed to match the directory structure expected by analysis and plotting code, so you should be able to unzip them into the appropriate directories rather than a new directory (e.g. using `unzip -d`).