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1204f1faba
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added scripts and files to make AA index work for all drug targets, add header to the aa index output and fetch the aa index headers
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2022-06-15 11:24:07 +01:00 |
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03321c261e
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working new_aa.sh
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2022-06-13 22:05:41 +01:00 |
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c4ae6d2412
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improved aa script
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2022-06-13 21:48:44 +01:00 |
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2307a19d86
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added example bash cmds
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2022-06-13 21:22:49 +01:00 |
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40c4d382f4
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added eg to run aaindex from a diff dir
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2022-06-13 21:15:12 +01:00 |
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bd7d01c7e6
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various aa_index_scripts
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2022-06-13 09:42:48 +01:00 |
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0c316e4a41
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renamed aa_index folder to aa_index_scripts
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2022-05-30 02:24:54 +01:00 |
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650d357afc
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reran to output merged_df3 and merged_df2 csvs from count_vars.ML
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2022-05-29 03:10:51 +01:00 |
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f41cd0082e
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moved mmcsm_provean_ed_combine_CHECKS.py to scratch for when I need ED data for merging
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2022-05-25 23:45:01 +01:00 |
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1baf7fa9f0
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lf
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2022-05-25 23:44:13 +01:00 |
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8e65d75b58
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added checks before comnining provean and mmcsm_lig
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2022-05-25 08:51:37 +01:00 |
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a2bcc3a732
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added mmcsm_lig and provean dfs merges in comnining_df.py
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2022-05-25 08:50:33 +01:00 |
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d8041fb494
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added count_vars_ML.R to check numbers for revised counts
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2022-05-05 19:32:34 +01:00 |
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39566ceadd
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lineage labels gsub now redundant in combining_dfs_plotting.R
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2022-05-05 19:31:00 +01:00 |
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d61d11e020
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Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis
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2022-05-05 13:36:03 +01:00 |
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e54ae877a8
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updated data extraction to ensure genes without common mutations and duplicate indices can run from the cmd
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2022-05-05 13:35:24 +01:00 |
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4f22cd3db1
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various tweaks to make the RShiny dashboards work
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2022-04-28 20:21:03 +01:00 |
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5429b8fed7
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saving data extraction updated script
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2022-04-28 13:02:30 +01:00 |
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e419d320ac
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saving data extraction with final processing
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2022-04-27 12:09:14 +01:00 |
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3c436f0c27
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finally revised data processing is complete
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2022-04-27 11:09:36 +01:00 |
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ac0d14e116
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done but getting an error when running from cmd
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2022-04-26 17:03:40 +01:00 |
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29e9d10e39
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add chek for lin index duplicates before output
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2022-04-25 18:38:04 +01:00 |
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1371704685
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got to the lineage extraction bit
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2022-04-25 18:37:01 +01:00 |
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0867827ec6
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saved section for generating revised dst
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2022-04-25 16:51:28 +01:00 |
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cb93cef3c7
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did all other mappings until dst column
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2022-04-23 11:14:34 +01:00 |
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7a10b4f223
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phewwww! finally resolved counts for ambiguous muts
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2022-04-22 17:51:11 +01:00 |
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3cd7b36c59
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updated data_extraction
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2022-04-22 15:18:08 +01:00 |
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bf7060baa9
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finally added all the lineage calculations
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2022-04-15 14:41:04 +01:00 |
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95a73efdd2
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saving work with sections reflecting activities
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2022-04-14 19:43:14 +01:00 |
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e99c169b35
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saving work, lineage bits are all over the place, need to rerrange
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2022-04-14 19:39:47 +01:00 |
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ae3a5500c9
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mostly done, now adding lineage magicry
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2022-04-14 19:27:21 +01:00 |
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f05cb96346
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added sections and slotted relevant bits from data_extraction to v2
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2022-04-14 12:21:16 +01:00 |
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e6faf80c20
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updating ambiguous muts manipulation section in data_extraction_v2
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2022-04-14 10:36:08 +01:00 |
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6330a2e716
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added v2 for data extraction
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2022-04-14 10:16:12 +01:00 |
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2518556c96
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added str.strip() instead of str.lstrip()
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2022-04-08 17:05:24 +01:00 |
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ac78fe16cd
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logoP SNP adj
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2022-03-06 14:48:53 +00:00 |
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56a6aa8c7e
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lineage_dist: add all_lineages feature
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2022-03-06 13:31:43 +00:00 |
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8fa585417e
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tweaks for params
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2022-03-02 19:42:24 +00:00 |
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bf3194259e
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lineage: toggle for "all lineages"
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2022-03-02 15:54:09 +00:00 |
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6c6709e41e
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various changes
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2022-03-02 11:44:04 +00:00 |
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2274f01f23
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combined msa and wt seq into 1 list so only list is passed as an arg for plotting ED plots
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2022-02-15 08:31:58 +00:00 |
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d38521e03a
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added placeholder defaults for functions in R to make sure that R shiny layput works with a data set for meeting tomorrow
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2022-02-14 19:33:00 +00:00 |
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0460ca1708
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added consurf plot function and corresponding test script
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2022-02-14 11:16:30 +00:00 |
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18e1f14455
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saving changes
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2022-02-14 11:14:40 +00:00 |
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6ffb084546
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added hbond residues in config for all genes
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2022-02-09 15:59:18 +00:00 |
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7a14655ecb
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added active site positions to all config.R
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2022-02-03 18:02:27 +00:00 |
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04cddbbf2b
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minor formatting, taken a line off the barplots_subcolours_aa_PS.R
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2022-02-02 19:01:13 +00:00 |
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3e5191f5c6
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attempting to visualise consurf plot along with highlighting active site pos
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2022-02-02 19:00:23 +00:00 |
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9c3818fd98
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added NOTE to the barplots_subcolours_aa_PS.R as I am trying it for other plots
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2022-02-02 18:59:33 +00:00 |
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d13484e8f5
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added function lineage_plot_data.R and corresponding test script, also renamed corr_plot_df.R to corr_plot_data and corresponing test script
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2022-02-01 16:25:58 +00:00 |
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