| 4696899 | Chase W. Nelson | 01 October 2020, 17:39 UTC | Updated README with eLife citation | 01 October 2020, 17:39 UTC |
| 0b9f8cb | Chase W. Nelson | 27 September 2020, 09:29 UTC | Update with link to Zenodo | 27 September 2020, 09:29 UTC |
| 3b28bcc | Chase W. Nelson | 25 September 2020, 11:01 UTC | Updated riboseq script documentation with Unix command | 25 September 2020, 11:01 UTC |
| 7cdd041 | Chase W. Nelson | 21 September 2020, 09:53 UTC | Initial commit: figure 7 and 8 scripts | 21 September 2020, 09:53 UTC |
| 3863646 | Chase W. Nelson | 20 September 2020, 09:23 UTC | Update README.md | 20 September 2020, 09:23 UTC |
| 326cbef | Chase W. Nelson | 19 September 2020, 19:21 UTC | Update README.md | 19 September 2020, 19:21 UTC |
| fc6aa35 | Chase W. Nelson | 19 September 2020, 19:19 UTC | Update README.md Added missing TOC | 19 September 2020, 19:19 UTC |
| d766871 | Chase W. Nelson | 19 September 2020, 19:15 UTC | Update README.md | 19 September 2020, 19:15 UTC |
| a4f43e4 | Chase W. Nelson | 19 September 2020, 19:12 UTC | Move data for Zotero instead; update README | 19 September 2020, 19:12 UTC |
| 0a08d62 | Chase W. Nelson | 19 September 2020, 18:12 UTC | Initial commit: selection_vs_expression.R | 19 September 2020, 18:12 UTC |
| e5b2a5f | Chase W. Nelson | 19 September 2020, 17:45 UTC | Initial commit: mass-spec_vs_riboseq.R | 19 September 2020, 17:45 UTC |
| 1893546 | Chase W. Nelson | 19 September 2020, 12:49 UTC | Update cover image | 19 September 2020, 12:49 UTC |
| d7b9917 | Chase W. Nelson | 18 September 2020, 18:27 UTC | Update README.md Fix formatting TOC | 18 September 2020, 18:27 UTC |
| ecdd128 | Chase W. Nelson | 18 September 2020, 18:26 UTC | Update README.md Less busy TOC | 18 September 2020, 18:26 UTC |
| 4378867 | Chase W. Nelson | 18 September 2020, 18:23 UTC | Initial commit: selection_sliding_windows.R script and data | 18 September 2020, 18:23 UTC |
| c33d71c | Chase W. Nelson | 18 September 2020, 17:38 UTC | Move all scripts to a /scripts/ subdirectory | 18 September 2020, 17:38 UTC |
| 42d4c41 | Chase W. Nelson | 18 September 2020, 17:36 UTC | Initial commit: riboseq.R | 18 September 2020, 17:36 UTC |
| 220c7b7 | Chase W. Nelson | 18 September 2020, 16:23 UTC | Initial commit: hydrophobicity profiles scripts and data | 18 September 2020, 16:23 UTC |
| 53ecff7 | Chase W. Nelson | 18 September 2020, 10:57 UTC | Update README.md Indented examples | 18 September 2020, 10:57 UTC |
| 8d10c02 | Chase W. Nelson | 18 September 2020, 10:54 UTC | Initial commit: three_levels_diversity.R and data | 18 September 2020, 10:54 UTC |
| 83fac3d | Chase W. Nelson | 18 September 2020, 10:22 UTC | Update temporal_pi.R | 18 September 2020, 10:22 UTC |
| a5fe425 | Chase W. Nelson | 18 September 2020, 09:24 UTC | Update cover_image.png | 18 September 2020, 09:24 UTC |
| 14ed732 | Chase W. Nelson | 18 September 2020, 08:46 UTC | Update README.md | 18 September 2020, 08:46 UTC |
| 241c410 | Chase W. Nelson | 18 September 2020, 08:41 UTC | Upload randomized peptides and short unannotated ORFs | 18 September 2020, 08:41 UTC |
| 22031f3 | Chase W. Nelson | 18 September 2020, 08:25 UTC | Initial commit: epitope data and scripts | 18 September 2020, 08:25 UTC |
| 4493f82 | Chase W. Nelson | 18 September 2020, 06:41 UTC | Create .gitignore | 18 September 2020, 06:41 UTC |
| 6aba08a | Chase W. Nelson | 18 September 2020, 06:39 UTC | Update cover_image.png | 18 September 2020, 06:39 UTC |
| 36f496b | Chase W. Nelson | 18 September 2020, 06:34 UTC | Update cover_image.png | 18 September 2020, 06:34 UTC |
| c0c13bf | Chase W. Nelson | 18 September 2020, 06:27 UTC | Update cover image and acknowledgments | 18 September 2020, 06:27 UTC |
| 76498d4 | Chase W. Nelson | 18 September 2020, 06:23 UTC | Update README.md | 18 September 2020, 06:23 UTC |
| b24803c | Chase W. Nelson | 18 September 2020, 06:22 UTC | Update cover_image.png | 18 September 2020, 06:22 UTC |
| 86219d7 | Chase W. Nelson | 18 September 2020, 06:19 UTC | Update README.md | 18 September 2020, 06:19 UTC |
| c1b0226 | Chase W. Nelson | 18 September 2020, 06:18 UTC | Update cover_image.png | 18 September 2020, 06:18 UTC |
| ff99812 | Chase W. Nelson | 18 September 2020, 06:16 UTC | Update README.md | 18 September 2020, 06:16 UTC |
| 61e0c94 | Chase W. Nelson | 18 September 2020, 06:15 UTC | Update cover_image.png | 18 September 2020, 06:15 UTC |
| 4871ba6 | Chase W. Nelson | 18 September 2020, 06:12 UTC | Update README.md | 18 September 2020, 06:12 UTC |
| 0078bdb | Chase W. Nelson | 18 September 2020, 06:12 UTC | Cover image | 18 September 2020, 06:12 UTC |
| 4af19ff | Chase W. Nelson | 18 September 2020, 06:09 UTC | Add cover image, revise README | 18 September 2020, 06:09 UTC |
| ae6cc1d | Chase W. Nelson | 17 September 2020, 18:37 UTC | Initial commit: extract_positions_by_timepoint.py | 17 September 2020, 18:37 UTC |
| 08a4450 | Chase W. Nelson | 17 September 2020, 18:22 UTC | Initial commit: extract_seqs_by_location.py | 17 September 2020, 18:22 UTC |
| e1f1df1 | Chase W. Nelson | 17 September 2020, 10:53 UTC | Update README.md Reorder Figure 5 scripts | 17 September 2020, 10:53 UTC |
| 8e5ee4a | Chase W. Nelson | 17 September 2020, 10:51 UTC | Initial commit: temporal_pi.R | 17 September 2020, 10:51 UTC |
| 1fa17e5 | Chase W. Nelson | 17 September 2020, 10:13 UTC | Initial commit: extract_seqs_by_timepoint.py | 17 September 2020, 10:13 UTC |
| 23cd1f4 | Chase W. Nelson | 17 September 2020, 09:57 UTC | Initial commit: extract_variable_columns_MSA* and create data directory | 17 September 2020, 09:57 UTC |
| d6fadf3 | Chase W. Nelson | 17 September 2020, 09:19 UTC | Update README.md | 17 September 2020, 09:19 UTC |
| 1234efc | Chase W. Nelson | 17 September 2020, 09:16 UTC | Update README.md Added SNPGenie reference; formatted examples as full Shell code blocks | 17 September 2020, 09:16 UTC |
| 4fbf1d9 | Chase W. Nelson | 17 September 2020, 09:06 UTC | Initial commit: extract_fasta_by_sites.pl | 17 September 2020, 09:06 UTC |
| a3db4d6 | Chase W. Nelson | 17 September 2020, 08:46 UTC | Initial commit: aligned_fasta2haplotypes.pl | 17 September 2020, 08:46 UTC |
| 9ff78d9 | Chase W. Nelson | 17 September 2020, 08:27 UTC | Initial commit: translate_nt_seq_file.pl | 17 September 2020, 08:27 UTC |
| 8cc9472 | Chase W. Nelson | 17 September 2020, 08:13 UTC | Initial commit: summarize_intrahost_by_site.py | 17 September 2020, 08:13 UTC |
| 01a90c9 | Chase W. Nelson | 17 September 2020, 07:45 UTC | Initial commit: generate_seqs_from_VCF.py | 17 September 2020, 07:45 UTC |
| 185604d | Chase W. Nelson | 17 September 2020, 07:29 UTC | Initial commit: filter_vcf.py | 17 September 2020, 07:29 UTC |
| 6a831c2 | Chase W. Nelson | 17 September 2020, 06:25 UTC | Initial commit: extract_seq_subset.py | 17 September 2020, 06:25 UTC |
| 2b5b387 | Chase W. Nelson | 16 September 2020, 18:34 UTC | Initial commit: tally_epitope_coverage.py | 16 September 2020, 18:34 UTC |
| 9c66d6d | Chase W. Nelson | 16 September 2020, 18:23 UTC | Initial commit: generate_random_protein.py | 16 September 2020, 18:23 UTC |
| 3530901 | Chase W. Nelson | 16 September 2020, 18:07 UTC | Initial commit: supplementary data | 16 September 2020, 18:07 UTC |
| bdc9bd8 | Chase W. Nelson | 16 September 2020, 17:45 UTC | Initial commit: riboseq_sliding_window.R | 16 September 2020, 17:45 UTC |
| db2851a | Chase W. Nelson | 16 September 2020, 17:34 UTC | Initial commit of ORF_length.R Upload the script and its documentation, input, and output; add Schlub reference | 16 September 2020, 17:34 UTC |
| 02a7c5a | Chase W. Nelson | 16 September 2020, 10:27 UTC | Update README.md Removed superfluous punctuation | 16 September 2020, 10:27 UTC |
| f7e3b0d | Chase W. Nelson | 16 September 2020, 10:26 UTC | Update README.md Introduced TOC; began documenting scripts; added acknowledgments, citation, contact information, and reference sections | 16 September 2020, 10:26 UTC |
| 07c4dfa | Chase W. Nelson | 09 August 2020, 08:35 UTC | Initial commit | 09 August 2020, 08:35 UTC |
