| 2126f52 | Nicholas Wu | 12 December 2021, 06:28:43 UTC | upxdate URL | 12 December 2021, 06:28:43 UTC |
| a084baf | Yiquan Wang | 26 November 2021, 18:43:15 UTC | Update README.md | 26 November 2021, 18:43:15 UTC |
| 2f0fab8 | Yiquan | 17 November 2021, 04:32:13 UTC | plot Flu B charge frequency | 17 November 2021, 04:32:13 UTC |
| 91224a0 | Yiquan | 17 November 2021, 04:31:24 UTC | update CA to sidechain | 17 November 2021, 04:31:24 UTC |
| 60da4c9 | Yiquan | 17 November 2021, 04:30:41 UTC | plot trajectory | 17 November 2021, 04:30:41 UTC |
| 3a87d01 | Yiquan | 17 November 2021, 04:30:29 UTC | add plot for additive only model | 17 November 2021, 04:30:29 UTC |
| 3510236 | Yiquan | 17 November 2021, 04:30:11 UTC | change to sidechain distance | 17 November 2021, 04:30:11 UTC |
| 7e2ee3b | Yiquan | 17 November 2021, 04:29:51 UTC | change to plot charge frequency | 17 November 2021, 04:29:51 UTC |
| a926f28 | Yiquan | 17 November 2021, 04:29:11 UTC | updating | 17 November 2021, 04:29:11 UTC |
| c9d755c | Yiquan | 17 November 2021, 04:27:12 UTC | change to sidechain distance | 17 November 2021, 04:27:12 UTC |
| e62f959 | Yiquan | 17 November 2021, 04:26:11 UTC | add fluB | 17 November 2021, 04:26:11 UTC |
| 9797642 | Yiquan | 17 November 2021, 04:25:57 UTC | model evolutionary trajectory | 17 November 2021, 04:25:57 UTC |
| d01e9cf | Yiquan | 17 November 2021, 04:25:39 UTC | change to analyse distance of sidechain | 17 November 2021, 04:25:39 UTC |
| 27aec56 | Yiquan | 17 November 2021, 04:24:53 UTC | additive model only regression | 17 November 2021, 04:24:53 UTC |
| f55fb27 | Yiquan Wang | 01 August 2021, 19:04:30 UTC | Update README.md | 01 August 2021, 19:04:30 UTC |
| da61afa | Yiquan | 01 August 2021, 19:03:26 UTC | coevolution score with filter | 01 August 2021, 19:03:26 UTC |
| 4a57517 | Yiquan | 01 August 2021, 19:01:20 UTC | Merge remote-tracking branch 'origin/master' | 01 August 2021, 19:01:20 UTC |
| c05a10c | Yiquan | 01 August 2021, 19:00:27 UTC | remove low coevolution score filter | 01 August 2021, 19:00:27 UTC |
| 2e32ae4 | Yiquan | 01 August 2021, 19:00:00 UTC | update library bug | 01 August 2021, 19:00:00 UTC |
| 5218518 | Yiquan | 01 August 2021, 18:59:32 UTC | plot the coevolution score distribution with filter | 01 August 2021, 18:59:32 UTC |
| 229a2f0 | Yiquan | 01 August 2021, 18:59:02 UTC | add peak distance filter | 01 August 2021, 18:59:02 UTC |
| dec7dc8 | Yiquan | 01 August 2021, 18:58:38 UTC | update result | 01 August 2021, 18:58:38 UTC |
| 970379a | Nicholas Wu | 01 August 2021, 01:36:13 UTC | update natural local charge analysis | 01 August 2021, 01:36:13 UTC |
| 2e82c47 | Yiquan | 25 July 2021, 18:54:56 UTC | add package | 25 July 2021, 18:54:56 UTC |
| 218d0e8 | Yiquan Wang | 15 July 2021, 02:04:51 UTC | Update README.md | 15 July 2021, 02:04:51 UTC |
| e65e897 | Yiquan Wang | 14 July 2021, 20:59:19 UTC | Update README.md | 14 July 2021, 20:59:19 UTC |
| 0f4da9e | Yiquan Wang | 14 July 2021, 20:58:26 UTC | Update README.md | 14 July 2021, 20:58:26 UTC |
| d447c6d | Yiquan Wang | 14 July 2021, 20:57:15 UTC | Update README.md | 14 July 2021, 20:57:15 UTC |
| 1bc550e | Yiquan | 14 July 2021, 20:55:17 UTC | Merge remote-tracking branch 'origin/master' | 14 July 2021, 20:55:17 UTC |
| a8a64e9 | Yiquan | 14 July 2021, 20:55:03 UTC | add comments | 14 July 2021, 20:55:03 UTC |
| 4e83455 | Yiquan | 14 July 2021, 20:54:36 UTC | add spearman cor | 14 July 2021, 20:54:36 UTC |
| a0a247e | Yiquan | 14 July 2021, 20:54:06 UTC | add result files | 14 July 2021, 20:54:06 UTC |
| cc313c9 | Yiquan Wang | 14 July 2021, 20:53:36 UTC | Update README.md | 14 July 2021, 20:53:36 UTC |
| 575d8f0 | Yiquan Wang | 14 July 2021, 19:10:04 UTC | Update README.md | 14 July 2021, 19:10:04 UTC |
| f606986 | Yiquan Wang | 10 July 2021, 22:19:55 UTC | Update README.md | 10 July 2021, 22:19:55 UTC |
| f687e2a | Yiquan Wang | 07 July 2021, 23:10:46 UTC | Create README.md | 07 July 2021, 23:10:46 UTC |
| 703a398 | Yiquan | 06 July 2021, 19:44:40 UTC | add figure | 06 July 2021, 19:44:40 UTC |
| b1acbe8 | Yiquan | 06 July 2021, 19:40:10 UTC | add HA correlation heatmap of additive fitness and epistasis across different strains | 06 July 2021, 19:40:10 UTC |
| 0af183e | Yiquan | 06 July 2021, 19:39:33 UTC | update HA regression output pathway | 06 July 2021, 19:39:33 UTC |
| c5de0f3 | Yiquan | 06 July 2021, 19:17:21 UTC | plot frequency of charge states over year | 06 July 2021, 19:17:21 UTC |
| b15f1ae | Yiquan | 06 July 2021, 19:15:50 UTC | update plot | 06 July 2021, 19:15:50 UTC |
| d807e3e | Yiquan | 06 July 2021, 19:15:37 UTC | updated | 06 July 2021, 19:15:37 UTC |
| 60aa0bf | Yiquan | 06 July 2021, 19:15:27 UTC | update natural variants fitness over year | 06 July 2021, 19:15:27 UTC |
| 9e4ed99 | Yiquan | 06 July 2021, 19:13:59 UTC | plot natural motifs(variants) frequency | 06 July 2021, 19:13:59 UTC |
| bca4e41 | Yiquan | 06 July 2021, 19:12:49 UTC | NA WT titer bar plot | 06 July 2021, 19:12:49 UTC |
| a5b5eab | Yiquan | 06 July 2021, 19:12:24 UTC | plot HA and NA mutation over year | 06 July 2021, 19:12:24 UTC |
| 5bc5217 | Yiquan | 06 July 2021, 19:12:06 UTC | plot how hyperparameter affect R/r2 | 06 July 2021, 19:12:06 UTC |
| d4a3800 | Yiquan | 06 July 2021, 19:11:33 UTC | plot frequency change | 06 July 2021, 19:11:33 UTC |
| 288a549 | Yiquan | 06 July 2021, 19:11:02 UTC | plot relationship of epistasis vs coevolution score | 06 July 2021, 19:11:02 UTC |
| d5bf631 | Yiquan | 06 July 2021, 19:10:29 UTC | plot for epistasis heatmap classified by charge state | 06 July 2021, 19:10:29 UTC |
| cb8b5dd | Yiquan | 06 July 2021, 19:09:54 UTC | update plot of epistasis heatmap | 06 July 2021, 19:09:54 UTC |
| 2c603a5 | Yiquan | 06 July 2021, 19:09:37 UTC | Plot relationship of Calpha distance vs epistasis | 06 July 2021, 19:09:37 UTC |
| 0a74355 | Yiquan | 06 July 2021, 19:08:50 UTC | Plot correlation of HA epistasis across different strains | 06 July 2021, 19:08:50 UTC |
| 3fb1323 | Yiquan | 06 July 2021, 19:08:02 UTC | Plot correlation of epistasis across different strains | 06 July 2021, 19:08:02 UTC |
| 6ad2e8e | Yiquan | 06 July 2021, 19:07:15 UTC | update plot comparison of fitness library | 06 July 2021, 19:07:15 UTC |
| 77a7eec | Yiquan | 06 July 2021, 19:05:50 UTC | update plot fitness vs charge | 06 July 2021, 19:05:50 UTC |
| e4081a9 | Yiquan | 06 July 2021, 19:05:26 UTC | update plot natural strain sequence vs charge | 06 July 2021, 19:05:26 UTC |
| ec27508 | Yiquan | 06 July 2021, 19:04:52 UTC | update plot additive fitness heatmap | 06 July 2021, 19:04:52 UTC |
| d1740d2 | Yiquan | 06 July 2021, 19:04:29 UTC | pymol script for plotting structure interaction within NA antigenic region of interest | 06 July 2021, 19:04:29 UTC |
| 278078a | Yiquan | 06 July 2021, 19:03:57 UTC | pymol script for plotting antigenic region on NA head domain | 06 July 2021, 19:03:57 UTC |
| dea8c55 | Yiquan | 06 July 2021, 19:03:19 UTC | pymol script for plotting NA head domain | 06 July 2021, 19:03:19 UTC |
| 1891186 | Yiquan | 06 July 2021, 19:02:44 UTC | one example of frequency change for diagram | 06 July 2021, 19:02:44 UTC |
| fc03296 | Yiquan | 06 July 2021, 19:02:07 UTC | accumulation of mutation on HA and NA of H3N2 strain over year | 06 July 2021, 19:02:07 UTC |
| 107a47a | Yiquan | 06 July 2021, 19:01:25 UTC | HA regression modeling | 06 July 2021, 19:01:25 UTC |
| c2e9d59 | Yiquan | 06 July 2021, 19:01:07 UTC | Coevolution score analysis of natural strain sequence | 06 July 2021, 19:01:07 UTC |
| ddad1f0 | Yiquan | 06 July 2021, 19:00:28 UTC | update regularization and other hyper parameter optimization | 06 July 2021, 19:00:28 UTC |
| 2d02f6e | Yiquan | 06 July 2021, 18:59:43 UTC | Calpha distance between NA antigenic regions | 06 July 2021, 18:59:43 UTC |
| e4e3d8e | Yiquan | 06 July 2021, 18:59:04 UTC | deleted | 06 July 2021, 18:59:04 UTC |
| b41237a | Yiquan | 06 July 2021, 18:58:35 UTC | updated plot | 06 July 2021, 18:58:35 UTC |
| eaf8c7e | Yiquan | 02 June 2021, 02:21:51 UTC | add filter of same charge sweep | 02 June 2021, 02:21:51 UTC |
| da50823 | Yiquan | 02 June 2021, 02:21:14 UTC | script to plot the correlation of natural peak_epi and model_epi | 02 June 2021, 02:21:14 UTC |
| f7d5051 | Yiquan | 02 June 2021, 02:19:52 UTC | update graph | 02 June 2021, 02:19:52 UTC |
| af77ad7 | Yiquan | 27 May 2021, 18:11:02 UTC | update compare repeat and library comparison | 27 May 2021, 18:11:02 UTC |
| 476bece | Yiquan | 27 May 2021, 18:09:48 UTC | fix the x axis text overlapping issue | 27 May 2021, 18:09:48 UTC |
| 2e572c0 | Yiquan | 26 May 2021, 00:29:05 UTC | add classifying the EPI by charge and plot | 26 May 2021, 00:29:05 UTC |
| 8a7660c | Yiquan | 26 May 2021, 00:28:28 UTC | add compare peak difference(years) for pairwise residues | 26 May 2021, 00:28:28 UTC |
| 4ceb324 | Yiquan | 26 May 2021, 00:27:22 UTC | updated | 26 May 2021, 00:27:22 UTC |
| 0e1d62d | Yiquan | 26 May 2021, 00:27:10 UTC | update images | 26 May 2021, 00:27:10 UTC |
| 158e697 | Yiquan | 25 May 2021, 04:47:39 UTC | Merge remote-tracking branch 'origin/master' | 25 May 2021, 04:47:39 UTC |
| 00e8dca | Yiquan | 25 May 2021, 04:44:21 UTC | add calculate the change peak | 25 May 2021, 04:44:21 UTC |
| 603271d | Nicholas Wu | 25 May 2021, 04:00:53 UTC | add charge analysis | 25 May 2021, 04:00:53 UTC |
| 112538c | Nicholas Wu | 25 May 2021, 02:02:09 UTC | filter out motifs that are not in lib | 25 May 2021, 02:02:09 UTC |
| 112f0e3 | Yiquan | 25 May 2021, 01:34:45 UTC | add epi heatmap | 25 May 2021, 01:34:45 UTC |
| d3406ba | Yiquan | 24 May 2021, 22:26:57 UTC | change output name | 24 May 2021, 22:26:57 UTC |
| 4ec18b1 | Yiquan | 24 May 2021, 22:26:26 UTC | fix the weight bug | 24 May 2021, 22:26:26 UTC |
| ad1d1d0 | Yiquan | 24 May 2021, 21:26:03 UTC | change to mean fit | 24 May 2021, 21:26:03 UTC |
| b7fc121 | Yiquan | 24 May 2021, 21:25:32 UTC | update calculate fit_evol by weight frequency | 24 May 2021, 21:25:32 UTC |
| f3ab888 | Yiquan | 24 May 2021, 19:58:21 UTC | update setting common legend | 24 May 2021, 19:58:21 UTC |
| 95233e3 | Yiquan | 24 May 2021, 03:02:16 UTC | Self Organizing Maps(SOM) and K mean for time series mutation frequency change residues clustering | 24 May 2021, 03:02:16 UTC |
| a29a143 | Yiquan | 24 May 2021, 03:00:48 UTC | plot residues frequency by years | 24 May 2021, 03:00:48 UTC |
| 3768fc7 | Yiquan | 24 May 2021, 02:59:41 UTC | calculate the sweep of mutation frequency by years | 24 May 2021, 02:59:41 UTC |
| 92cd667 | Yiquan | 24 May 2021, 02:58:18 UTC | calculate the motif by year and preference evolve | 24 May 2021, 02:58:18 UTC |
| 90a5f0c | Yiquan | 24 May 2021, 02:56:12 UTC | plot preference by years | 24 May 2021, 02:56:12 UTC |
| ee4dd76 | Yiquan | 24 May 2021, 02:55:45 UTC | calculate the preference and motif average fitness | 24 May 2021, 02:55:45 UTC |
| 3cc5c9d | Yiquan | 24 May 2021, 02:54:41 UTC | calculate the mutant frequency change by years | 24 May 2021, 02:54:41 UTC |
| 52d7226 | Yiquan | 20 May 2021, 21:25:00 UTC | update heatmap epistasis plot script | 20 May 2021, 21:25:00 UTC |
| c9155f6 | Yiquan | 20 May 2021, 21:24:34 UTC | update heatmap additive fitness plot script | 20 May 2021, 21:24:34 UTC |
| 4904db2 | Yiquan | 20 May 2021, 21:24:07 UTC | add the heatmap of epi and add | 20 May 2021, 21:24:07 UTC |
| 0f9c9b3 | Yiquan | 20 May 2021, 02:18:18 UTC | update how reg affect prediction R2 | 20 May 2021, 02:18:18 UTC |
| 7260b43 | Yiquan | 20 May 2021, 02:17:10 UTC | update how single variant bs/lr/reg affects additive fitness/epistasis R and prediction R2 | 20 May 2021, 02:17:10 UTC |
