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