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LSHTM_analysis/scripts
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Tanushree Tunstall bdbc97c40a fix many plot functions to stop them using the "g=ggplot()" pattern, 
which annoyingly throws away lots of useful data that RShiny needs for
clickable plots. Also split the "flame bar" for ligand distance out into
separate functions in generate_distance_colour_map.R. This can now be
easily incorporated into any "wide" graph showing all positions.
2022-08-03 18:58:27 +01:00
..
aa_index_scripts 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 2022-06-15 11:24:07 +01:00
functions fix many plot functions to stop them using the "g=ggplot()" pattern, 2022-08-03 18:58:27 +01:00
ml added test_func_combined.py 2022-07-29 00:14:39 +01:00
my_pdbtools tidy up 2022-01-06 16:38:59 +00:00
plotting added replace b factor scripts for lig affinity and ppi2 2022-08-02 20:30:43 +01:00
redundant moved old af_or_calcs.R to redundant 2021-06-11 13:27:40 +01:00
aa_code.py added function to add aa code for mcsm and gwas style mutations to a given files 2021-06-18 17:48:26 +01:00
aa_prop.py 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 2021-06-14 13:24:00 +01:00
add_aa_prop.py 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 2021-06-14 13:24:00 +01:00
add_chains_pdb.py adding and saving files 2021-02-09 18:30:47 +00:00
af_or_calcs.R wholesale change for Header_TT.R location 2022-01-26 11:39:03 +00:00
combining_dfs.py added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py 2022-06-15 18:36:28 +01:00
combining_FIXME.py resolving merge conflicts dur to shoddy data 2020-07-14 14:09:42 +01:00
count.py saving before starting work 2021-06-04 09:38:17 +01:00
count_vars_ML.R added mut_landscape.R that outputs the mutational positions and annotations for generating the structural landscape of all gene-targets 2022-07-31 12:01:56 +01:00
data_extraction.py horrible lineage analysis hell 2022-06-28 21:51:02 +01:00
data_extraction_epistasis.py handled rpob 5uhc position offset in mcsm_ppi2 2022-01-04 10:45:29 +00:00
data_selective_pressure.R added af and OR columns in the data 2020-10-06 19:39:59 +01:00
deepddg_format.py bring in embb stuff which was in the wrong branch 2021-10-28 11:18:13 +01:00
DOCS added test2/ for testing updated foldx script 2021-02-10 10:16:28 +00:00
dssp_df.py updating notes to running_scripts.py as running for another drug-target 2020-11-17 13:55:16 +00:00
find_missense.py tidy script for linking or_kinship with missense variant info 2020-08-14 16:41:11 +01:00
gene_targets_names.txt just tested logo plot msa with embb after correcting the OMINOUS fasta file 2022-01-19 18:57:04 +00:00
Header_TT.R various changes 2022-03-02 11:44:04 +00:00
kd_df.py handled rpob 5uhc position offset in mcsm_ppi2 2022-01-04 10:45:29 +00:00
ks_test_all_PS.R more header_tt 2022-01-26 11:50:50 +00:00
ks_test_dr_others_PS.R more header_tt 2022-01-26 11:50:50 +00:00
ks_test_dr_PS.R more header_tt 2022-01-26 11:50:50 +00:00
mut_electrostatic_changes.py changed aa_prop_water to 3 categ according to KD, updated ref dict 2021-06-14 13:22:56 +01:00
mutate.py added mutate.py and run_mutate.sh to create MSA aligbments for mutant sequences required to generate logoplot from sequence in R 2020-09-14 15:17:49 +01:00
or_kinship_link.py resolving missing mutation info in combining script 2020-09-04 20:56:16 +01:00
pdb_data_exraction.py added script to interrogate pdb files mainly for res numbers 2020-11-16 16:01:31 +00:00
pdb_fasta_plot.R added pdb_fasta_plot.R for generating some useful plots for shiny 2021-08-17 10:55:06 +01:00
rd_df.py bring in embb stuff which was in the wrong branch 2021-10-28 11:18:13 +01:00
reference_dict.py changed aa_prop_water to 3 categ according to KD, updated ref dict 2021-06-14 13:22:56 +01:00
run_mutate.sh adding legend forlogo plot 2022-01-14 10:18:01 +00:00
run_mutate2.sh finding seq discrepancy in MSA for embb 2022-01-17 19:11:10 +00:00
running_scripts fixed cmd running script problem for logo plots 2021-06-24 12:12:36 +01:00
snpinfo_format.py script to format snp_info.txt 2020-08-21 13:23:29 +01:00
temp_results.py added test2/ for testing updated foldx script 2021-02-10 10:16:28 +00:00
tidy_split.py data extraction tidy up 2020-07-08 13:26:33 +01:00