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1155959e67
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added deep ddg formatted data to combinig_dfs.py
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2021-06-21 12:56:06 +01:00 |
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3ff9604002
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added deepddg data to combining_df.py
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2021-06-21 11:53:56 +01:00 |
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25fcebe448
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added function to add aa code for mcsm and gwas style mutations to a given files
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2021-06-18 17:48:26 +01:00 |
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926d181120
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saving work before adding files
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2021-06-18 17:47:09 +01:00 |
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0e0f7c89df
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Merge branch 'gidb_dev'
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2021-06-14 13:27:00 +01:00 |
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0881181f4b
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added aa_prop.py and add_aa_prop.py to add aa properties for wt and mutant in a given file containing one letter code wt and mut cols as csv
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2021-06-14 13:24:00 +01:00 |
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58b5b63595
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changed aa_prop_water to 3 categ according to KD, updated ref dict
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2021-06-14 13:22:56 +01:00 |
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2a8133898f
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added function and test for aa_prop_bp.R
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2021-06-14 09:22:05 +01:00 |
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140bdc6d96
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added example for layout
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2021-06-14 09:06:30 +01:00 |
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851683811e
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weird pdbtools commit
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2021-06-11 21:45:18 +01:00 |
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6dd8cc6f44
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added another aa dict type to reference_dict.py and calculated electrostatisc changes for muts based on adding these properties to mcsm mut stule snps. This will allow the calculation on a given file type since the ref dict can now easily be adapted.
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2021-06-11 17:12:21 +01:00 |
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6e8116bc16
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calculating af_or using function and cmd options now
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2021-06-11 15:12:08 +01:00 |
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5f82c8b393
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added script to test af_or_calcs
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2021-06-11 13:33:25 +01:00 |
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96af746726
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added mychisq_or.R and af_or_calcs.R
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2021-06-11 13:28:07 +01:00 |
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ad0b814f9c
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moved old af_or_calcs.R to redundant
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2021-06-11 13:27:40 +01:00 |
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587be435e9
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saving the correct af or script
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2021-06-11 13:26:28 +01:00 |
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4e38e2a80e
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saving work before converting to a function
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2021-06-11 13:25:02 +01:00 |
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d9e00b9a42
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minor tweak to plotting_globals.R to make gene_match a global var
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2021-06-11 11:21:20 +01:00 |
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29fa99b914
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moved functions/ in the scripts dir
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2021-06-11 11:11:39 +01:00 |
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2dc81e72f4
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moved old bp scripts to redundant
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2021-06-10 16:18:08 +01:00 |
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ff7522eca2
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moved plotting_func to functions and replaced 3 basic_barplots scripts with 1
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2021-06-10 16:09:58 +01:00 |
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b9d176afa4
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added function for position_count_bp.R
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2021-06-10 14:46:11 +01:00 |
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cbb3749a21
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added functions dir for further tidying and tested this with ind scripts for stability
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2021-06-09 18:13:18 +01:00 |
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912a439589
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moved bp function script to function/
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2021-06-09 17:08:56 +01:00 |
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826b8aa9d0
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added shiny app and turned stability bp to function
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2021-06-09 17:05:02 +01:00 |
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f871dd39cd
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saving work
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2021-06-09 16:27:05 +01:00 |
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47a6ddbf72
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repuposed and ran basic_barplots for lig and foldx including filenames
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2021-06-09 11:33:08 +01:00 |
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27d79105ef
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repurposed basic_barplots_foldx.R
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2021-06-09 11:24:50 +01:00 |
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8f73c7b804
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uddated how to run plotting scripts. This is a cleaner version to keep up-to-date
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2021-06-08 16:53:07 +01:00 |
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3f691281bc
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wrapper script basic_barplots_PS.R now takes cmd and calls functions to generate plots.Tested and verfiied.
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2021-06-08 16:48:19 +01:00 |
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1505a3c707
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tidied plotting_data.R as a function returning a lits of dfs
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2021-06-08 16:00:28 +01:00 |
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9af0249e0e
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added plotting_globals and text file with info on how to run plotting scripst
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2021-06-04 17:26:01 +01:00 |
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a5715bcccc
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tweaking baic bp to make generic
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2021-06-04 17:23:41 +01:00 |
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aaa24ca32d
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minor updates to dir.R
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2021-06-04 15:05:52 +01:00 |
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a1fef205da
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adpated combining_dfs.py and plotting.R for gid and attempting to make it generic
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2021-06-04 14:36:16 +01:00 |
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b77f55fcc2
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saving before starting work
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2021-06-04 09:38:17 +01:00 |
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59430a49dd
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updated counts.py with wt seq counts
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2021-03-03 11:54:48 +00:00 |
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88229860e2
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added adjusted p-values for DM muts comparison
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2021-02-27 10:42:04 +00:00 |
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9784bc1729
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updated count.py with indel and stop codon count
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2021-02-24 09:56:36 +00:00 |
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aca73048c1
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added count.py to count samples for quick checks
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2021-02-21 16:07:33 +00:00 |
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9b0d2f6550
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saving work and generating revised_figure7
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2021-02-20 16:17:38 +00:00 |
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e3189df74b
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dynamut scripts and minor change dir for rd_df.py
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2021-02-10 15:40:33 +00:00 |
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21451789e7
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renamed files
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2021-02-10 11:53:20 +00:00 |
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3280cdb2a1
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added test2/ for testing updated foldx script
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2021-02-10 10:16:28 +00:00 |
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4f25acfa35
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adding and saving files
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2021-02-09 18:30:47 +00:00 |
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a67156bc87
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test2 bugfixes
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2021-02-08 15:24:22 +00:00 |
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619a828659
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added chain_extract.py and pdb_chain_extract.py
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2020-11-30 14:11:46 +00:00 |
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a7d7bceb00
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adding options to specify files by user
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2020-11-27 13:02:15 +00:00 |
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50744f046f
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added my_pdbtools containing pdbtools cloned from a git repo
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2020-11-17 13:56:23 +00:00 |
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2911678177
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updating notes to running_scripts.py as running for another drug-target
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2020-11-17 13:55:16 +00:00 |
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