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e9fb582db9
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msa indexes
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2022-09-05 18:49:40 +01:00 |
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1241ad0b22
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various usability tweaks to LogoPlotMSA and position_annotation
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2022-09-05 16:06:10 +01:00 |
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f949592dd8
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added consurf_colours_no_isd to ensure consurf plots are not messed up in the absesnce of 0 categ
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2022-09-05 16:01:21 +01:00 |
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2cec743ae0
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added pnca plot dir to generate plots that weren#t covered in the paper
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2022-09-05 14:02:04 +01:00 |
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1dacebbaf6
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renamed files for lineage_diff_sensitivites.R
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2022-09-05 13:19:06 +01:00 |
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69a0da0a59
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added script for lineage diff sensitivities
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2022-09-04 21:36:49 +01:00 |
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58c25e23c0
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added ml_iterator.py
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2022-09-03 14:42:13 +01:00 |
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4976e9d8af
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saving
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2022-09-03 14:41:22 +01:00 |
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2b953583e2
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added combined model FS code and run script
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2022-09-03 12:28:36 +01:00 |
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78704dec5a
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saving
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2022-09-03 12:28:21 +01:00 |
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889bea1e63
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ran ml_iterator for actual genes
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2022-09-03 09:23:37 +01:00 |
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d77389acfc
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running combined model with FS
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2022-09-03 09:22:06 +01:00 |
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c7351970a2
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chmod
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2022-09-02 21:14:02 +01:00 |
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f9ce90e3f4
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saving
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2022-09-02 10:08:58 +01:00 |
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93e958ae6a
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now running for combined gene actual
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2022-09-02 10:04:27 +01:00 |
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00ca7a6b27
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tweaks
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2022-09-02 09:52:11 +01:00 |
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c845d96102
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added combined_model_iterator.py that has oversampling
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2022-09-02 09:50:51 +01:00 |
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338dd329e9
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running ml_iterator_CV for all targets with different CV threholds
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2022-09-01 16:29:32 +01:00 |
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80b4a1850c
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tested to make sure the cols added dont break code
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2022-09-01 16:23:57 +01:00 |
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de9e6a709b
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added 3 cols for snp counts for ML
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2022-09-01 16:11:23 +01:00 |
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2bf91681b4
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preparing to rerun ML iterator
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2022-09-01 13:41:02 +01:00 |
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56b71c6ca2
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added avg affinity and stability cols with mask for avg affinity
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2022-09-01 13:04:37 +01:00 |
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e03ce277b7
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checked masked cols after running
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2022-09-01 12:57:38 +01:00 |
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f9129b9ebc
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added nca dist criteria for masking
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2022-09-01 12:55:38 +01:00 |
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f94eadf1d4
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added
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2022-09-01 12:54:41 +01:00 |
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82e2da4f3b
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ml df stuff
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2022-09-01 11:39:11 +01:00 |
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c2b46286d8
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added rpob ks test script
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2022-08-31 22:03:39 +01:00 |
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bc9d1a7149
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added embb plotting scripts
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2022-08-31 22:03:07 +01:00 |
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a5d22540e1
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renamed count_vars_ML previous version as such
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2022-08-31 22:02:46 +01:00 |
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317b97bc9c
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stuff
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2022-08-30 12:10:56 +01:00 |
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d7f348318c
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removed template files from rpob
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2022-08-29 23:28:53 +01:00 |
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f39bbdcce7
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added katg and rpob files
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2022-08-29 23:27:37 +01:00 |
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7c2e4b898e
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added rpob plot scripts
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2022-08-29 23:27:13 +01:00 |
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8f97ab7cc8
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rpob
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2022-08-29 18:23:47 +01:00 |
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6441be21ab
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added katg tables
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2022-08-28 22:31:29 +01:00 |
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d5da923a74
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stuff
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2022-08-28 13:17:43 +01:00 |
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7bed6a1e22
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added all scripts
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2022-08-27 23:12:12 +01:00 |
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da8a1069a8
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saving work
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2022-08-27 23:12:12 +01:00 |
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c3067b9176
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gg pairs fixup for alr
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2022-08-27 17:15:40 +01:00 |
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927ab850a8
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added DCS to alr config
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2022-08-27 16:36:49 +01:00 |
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c6f5a446c3
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stuff
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2022-08-27 15:35:48 +01:00 |
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79b251047d
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allow position_annotation to specify colours
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2022-08-27 15:35:48 +01:00 |
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2cbc460f87
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added output tables with active site
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2022-08-26 21:50:33 +01:00 |
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f290d8ec9e
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addded appendix tables and frequent muts
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2022-08-25 22:21:05 +01:00 |
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741aad3dd1
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added nsSNPs to lineage dist plots
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2022-08-25 22:17:41 +01:00 |
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ca619bc662
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fix directory assumption
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2022-08-25 18:02:25 +01:00 |
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afa9166ca8
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things
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2022-08-25 17:58:04 +01:00 |
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cd76a4b919
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things
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2022-08-25 17:58:04 +01:00 |
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3b77b4b611
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stuff
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2022-08-25 17:58:04 +01:00 |
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e4e8bd7278
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added colors for tiles for gid plots and appendix tables
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2022-08-25 17:50:49 +01:00 |
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