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aa_index_scripts
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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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functions
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reran to generate merged_df3 with correct dst for dst muts. modified combining_dfs_plotting.R
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2022-07-08 21:33:57 +01:00 |
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ml
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added reverse traininig as split type in SplitTTS.py
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2022-07-11 20:03:06 +01:00 |
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my_pdbtools
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tidy up
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2022-01-06 16:38:59 +00:00 |
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plotting
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reran to generate merged_df3 with correct dst for dst muts. modified combining_dfs_plotting.R
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2022-07-08 21:33:57 +01:00 |
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redundant
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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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aa_code.py
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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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aa_prop.py
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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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add_aa_prop.py
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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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add_chains_pdb.py
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adding and saving files
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2021-02-09 18:30:47 +00:00 |
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af_or_calcs.R
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wholesale change for Header_TT.R location
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2022-01-26 11:39:03 +00:00 |
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combining_dfs.py
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added active site indication for merged_dfs in count_vars_ML.R and also added 'gene_name' in combining_dfs.py
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2022-06-15 18:36:28 +01:00 |
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combining_FIXME.py
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resolving merge conflicts dur to shoddy data
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2020-07-14 14:09:42 +01:00 |
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count.py
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saving before starting work
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2021-06-04 09:38:17 +01:00 |
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count_vars_ML.R
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reran to generate merged_df3 with correct dst for dst muts. modified combining_dfs_plotting.R
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2022-07-08 21:33:57 +01:00 |
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data_extraction.py
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horrible lineage analysis hell
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2022-06-28 21:51:02 +01:00 |
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data_extraction_epistasis.py
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handled rpob 5uhc position offset in mcsm_ppi2
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2022-01-04 10:45:29 +00:00 |
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data_selective_pressure.R
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added af and OR columns in the data
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2020-10-06 19:39:59 +01:00 |
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deepddg_format.py
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bring in embb stuff which was in the wrong branch
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2021-10-28 11:18:13 +01:00 |
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DOCS
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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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dssp_df.py
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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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find_missense.py
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tidy script for linking or_kinship with missense variant info
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2020-08-14 16:41:11 +01:00 |
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gene_targets_names.txt
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just tested logo plot msa with embb after correcting the OMINOUS fasta file
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2022-01-19 18:57:04 +00:00 |
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Header_TT.R
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various changes
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2022-03-02 11:44:04 +00:00 |
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kd_df.py
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handled rpob 5uhc position offset in mcsm_ppi2
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2022-01-04 10:45:29 +00:00 |
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ks_test_all_PS.R
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more header_tt
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2022-01-26 11:50:50 +00:00 |
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ks_test_dr_others_PS.R
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more header_tt
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2022-01-26 11:50:50 +00:00 |
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ks_test_dr_PS.R
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more header_tt
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2022-01-26 11:50:50 +00:00 |
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mut_electrostatic_changes.py
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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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mutate.py
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added mutate.py and run_mutate.sh to create MSA aligbments for mutant sequences required to generate logoplot from sequence in R
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2020-09-14 15:17:49 +01:00 |
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or_kinship_link.py
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resolving missing mutation info in combining script
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2020-09-04 20:56:16 +01:00 |
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pdb_data_exraction.py
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added script to interrogate pdb files mainly for res numbers
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2020-11-16 16:01:31 +00:00 |
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pdb_fasta_plot.R
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added pdb_fasta_plot.R for generating some useful plots for shiny
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2021-08-17 10:55:06 +01:00 |
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rd_df.py
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bring in embb stuff which was in the wrong branch
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2021-10-28 11:18:13 +01:00 |
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reference_dict.py
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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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run_mutate.sh
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adding legend forlogo plot
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2022-01-14 10:18:01 +00:00 |
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run_mutate2.sh
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finding seq discrepancy in MSA for embb
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2022-01-17 19:11:10 +00:00 |
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running_scripts
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fixed cmd running script problem for logo plots
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2021-06-24 12:12:36 +01:00 |
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snpinfo_format.py
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script to format snp_info.txt
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2020-08-21 13:23:29 +01:00 |
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temp_results.py
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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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tidy_split.py
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data extraction tidy up
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2020-07-08 13:26:33 +01:00 |
