This repository contains material under several licences. Which one applies depends on what the file is, as set out below. Files not listed under sections 3 or 4 fall under section 1 if they are code or documentation and section 2 if they are data or results. 1. Code and documentation: MIT License ====================================== Applies to the notebooks and scripts (tag-seq/code/, render-all.sh, check-reproduction.R, manuscript/check-placeholders.R, .github/), the project configuration (_quarto.yml, renv.lock, .Rprofile, CHECKSUMS.sha256), the landing page (index.qmd), and the documentation (README.md, REPRODUCIBILITY-PLAN.md, SUBMISSION-CHECKLIST.md, NOTES.md and the READMEs in each directory). MIT License Copyright (c) 2022-2026 The project-sockeye-tagseq contributors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 2. Data and results produced by this project: CC0 1.0 Universal =============================================================== Applies to the count matrices and phenotype tables (tag-seq/data/), and to every result this analysis produces: tag-seq/DESEQ_output/, tag-seq/gene_tables/, tag-seq/GO_output/, figures/ and manuscript/supplementary/. The quality-control reports in tag-seq/QC/ are covered too, subject to the note on them in section 4. The contributors have dedicated these files to the public domain by waiving all of their rights to them worldwide under copyright law, including all related and neighbouring rights, to the extent allowed by law. You can copy, modify, distribute and use them, even for commercial purposes, without asking permission. Citing the associated article or this repository (CITATION.cff) is requested as scholarly practice, not required. Full legal text: https://creativecommons.org/publicdomain/zero/1.0/legalcode 3. The manuscript: not licensed =============================== manuscript/manuscript.qmd, manuscript/cover-letter.qmd and their rendered outputs are a draft of an article intended for journal submission. They are not released under an open licence; the authors retain all rights pending publication. manuscript/references.bib is bibliographic metadata and may be reused freely. 4. Third-party material: its own terms ====================================== These files come from elsewhere and are not covered by sections 1-3. - tag-seq/genome/GCF_006149115.2_Oner_1.1_feature_table.txt and tag-seq/sequences/GCF_006149115.2_Oner_1.1_genomic-sequence-lengths.txt: derived from NCBI RefSeq assembly GCF_006149115.2. NCBI itself places no restrictions on the use or distribution of its data, though the original submitters of data may hold rights of their own; see https://www.ncbi.nlm.nih.gov/home/about/policies/. - tag-seq/genome/GCF_006149115.2_Oner_1.1_gene_ontology.gaf.gz: Gene Ontology annotation generated by NCBI. GO data are made available by the Gene Ontology Consortium under CC BY 4.0; see http://geneontology.org/docs/go-citation-policy/. - KEGG pathway data: not included. KEGG is not a public database: the API is provided for academic use by academic users, and non-academic use requires a licence; see https://www.kegg.jp/kegg/legal.html. The analysis downloads the two responses it needs at render time (tag-seq/genome/kegg_one_SOURCE.txt), and they are not distributed with this repository. The enrichment results derived from them (section 2) report pathway identifiers, names and gene counts, as a publication does. - manuscript/apa.csl: the APA 7th edition style from the Citation Style Language project, licensed CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0/). - manuscript/reference-manuscript.docx: derived from pandoc's default reference document, and subject to pandoc's licensing. - renv/activate.R: generated by renv (MIT, Posit Software, PBC). - archive/david-2023/: output of the DAVID web service, subject to DAVID's terms of use. - tag-seq/QC/multiqc_gonad/*.html: reports generated by MultiQC (GPL-3.0), which embed JavaScript libraries under their own licences. The data in them are covered by section 2.