Commit Graph

Select branches

Hide Pull Requests

Docker

main

#1

v1.0

v6.0

Mono Color

• a70558b880
  Fixed error with blast hits Godwin Ani 2024-04-26 14:24:36 -04:00
• bbe97c5888
  Add files via upload Godwin Ani 2024-04-26 14:23:55 -04:00
• 0eb002a1bd
  Update trees.py MCLeleu 2024-04-17 15:08:24 -04:00
• 18f4686223
  Fixing underscore/dot issue in trees.py Auden Cote-L'Heureux 2024-04-15 16:25:32 -04:00
• a1d92144e4
  Update README.md ElinorSterner 2024-04-14 16:55:19 -04:00
• 2f67243515
  Add files via upload Godwin Ani 2024-04-11 14:43:53 -04:00
• 8b35b8a64d
  Update CladeGrabbing_v3.2.py Godwin Ani 2024-04-05 13:14:14 -04:00
• 5bdd2730bf
  Rename CladeGrabbing_v2.1.py to CladeGrabbing_v3.2.py Godwin Ani 2024-04-05 13:14:03 -04:00
• e2134d08a3
  New version Godwin Ani 2024-04-05 13:13:23 -04:00
• 3f8bc48a3f
  Update ColorByClade_v2.2.py Godwin Ani 2024-04-01 11:11:06 -04:00
• a59cbe1102
  ColorByClade_v2.1.py to ColorByClade_v2.2.py Godwin Ani 2024-04-01 11:10:18 -04:00
• 81a46d2714
  Cannot set myself as outgroup catch Godwin Ani 2024-04-01 11:09:45 -04:00
• 21e54ab7e4
  Reverting to previous version Godwin Ani 2024-04-01 11:04:37 -04:00
• 13e6d300c5
  Adding keep_iter parameter Godwin Ani 2024-03-22 15:07:25 -04:00
• 80ad29e6d5
  Adding keep_iter parameter Godwin Ani 2024-03-22 15:05:54 -04:00
• f40873b6b0
  Update GuidanceWrapper_v2.1.py Godwin Ani 2024-03-19 13:26:41 -04:00
• 06ba70c0f7
  Update Iteration parameter Godwin Ani 2024-03-19 10:31:59 -04:00
• b91cf0fb63
  Iterations parameter added Godwin Ani 2024-03-19 10:29:41 -04:00
• b8a68098f3
  Fixing assembled transcript overwrite issue in 7b Auden Cote-L'Heureux 2024-03-18 10:16:31 -04:00
• 1dcb7f05dd
  Delete PTL1/Transcriptomes/Scripts/7b_SummaryStats.py Auden Cote-L'Heureux 2024-03-18 10:15:58 -04:00
• e87a10ad9b
  Add files via upload Adri K. Grow 2024-03-15 11:35:33 -04:00
• 97b9c8ee67
  Delete Utilities/for_taxonomy/ReadMapping_v2.0.py Adri K. Grow 2024-03-15 11:35:18 -04:00
• 87840891d6
  Add files via upload Adri K. Grow 2024-03-09 11:06:45 -05:00
• ce0649bf14
  Delete PTL2/run_phylotol.sh Adri K. Grow 2024-03-09 11:05:59 -05:00
• ca23f3f789
  Update ColorByClade_v2.1.py Katzlab 2024-02-20 16:48:44 -05:00
• 93b328306a
  Halfway done with fix to wrapper.py Auden Cote-L'Heureux 2024-02-16 14:10:14 -05:00
• 384dd72125
  Adding check to 4_InFrameStopCodonEstimator.py Auden Cote-L'Heureux 2024-02-16 14:06:06 -05:00
• 7ca7e378bc
  Update ColorByClade_v2.1.py Auden Cote-L'Heureux 2024-02-16 08:37:20 -05:00
• 710927f5fc
  Update CladeGrabbing_v2.1.py Katzlab 2024-02-14 17:46:48 -05:00
• 75b06a788e
  annotating concatenate.py Auden Cote-L'Heureux 2024-02-07 12:52:47 -05:00
• 920b3b4ad4
  annotating contamination.py Auden Cote-L'Heureux 2024-02-07 12:48:38 -05:00
• 23b81f83f7
  annotating trees.py Auden Cote-L'Heureux 2024-02-07 12:30:22 -05:00
• 7220b81402
  annotating guidance.py Auden Cote-L'Heureux 2024-02-07 12:18:46 -05:00
• 80409a22ff
  annotating preguidance.py Auden Cote-L'Heureux 2024-02-07 12:04:30 -05:00
• c00780e313
  annotating phylotol.py Auden Cote-L'Heureux 2024-02-07 11:52:42 -05:00
• c308864f5c
  annotating utils.py Auden Cote-L'Heureux 2024-02-07 11:52:08 -05:00
• b7a3d1ac12
  annotating phylotol.py Auden Cote-L'Heureux 2024-02-07 11:46:40 -05:00
• 0a7ab708b9
  Updating contamination loop parameters in utils.py Auden Cote-L'Heureux 2024-02-07 11:36:45 -05:00
• 877aabd2ef
  adding contamination loop back to wrapper Auden Cote-L'Heureux 2024-02-07 11:31:03 -05:00
• 0f2ae76d13
  exiting after errors in guidance.py Auden Cote-L'Heureux 2024-02-07 11:30:26 -05:00
• b981641f62
  removing calls to logger in trees.py Auden Cote-L'Heureux 2024-02-07 11:29:55 -05:00
• 556b8646ba
  removing calls to logger in guidance.py Auden Cote-L'Heureux 2024-02-07 11:28:07 -05:00
• 604a4af182
  Delete PTL2/Scripts/logger.py Auden Cote-L'Heureux 2024-02-07 11:25:06 -05:00
• fff0032c0d
  num_contams to float for proportional running contamination.py Auden Cote-L'Heureux 2024-02-07 11:24:54 -05:00
• 9844842aed
  Add files via upload Auden Cote-L'Heureux 2024-02-07 11:23:49 -05:00
• 00ee7e44b3
  Rename Plotcomps_speciesName_v1.0.R to Plotcomps_SppName_v1.0.R Godwin Ani 2024-02-05 14:22:29 -05:00
• f71f07a313
  Rename Plotcomps_speciesName.R to Plotcomps_speciesName_v1.0.R Godwin Ani 2024-02-05 14:21:59 -05:00
• 7865b6dfe7
  Add files via upload Godwin Ani 2024-02-05 14:19:00 -05:00
• f6cb9e95ff
  Update CountTaxonOccurence_v2.0.py Godwin Ani 2024-02-05 13:53:22 -05:00
• ded4143f11
  Rename CladeSizes_v3.0.py to CladeSizes_v2.0.py Godwin Ani 2024-02-05 13:51:38 -05:00
• 8be57a0231
  SharedOGs_v1.0.py Godwin Ani 2024-02-05 13:49:10 -05:00
• b6744e0f78
  Update SharedOGs_v1.0.py Godwin Ani 2024-02-05 13:48:49 -05:00
• 4ae1382815
  Update Cluster_v2.0.py Godwin Ani 2024-02-05 13:25:11 -05:00
• f6c34517ae
  Update Cluster_v2.0.py Godwin Ani 2024-02-05 13:23:10 -05:00
• 59b74bfa5f
  Update CladeGrabbing_v2.1.py Katzlab 2024-01-29 08:20:30 -05:00
• 835104592f
  Updating headers in CheckSetup.py Auden Cote-L'Heureux 2024-01-26 11:47:22 -05:00
• bf669310fd
  Updating header and Hook name check CheckSetup.py Auden Cote-L'Heureux 2024-01-26 11:46:06 -05:00
• df54de3589
  Updating header in wrapper.py Auden Cote-L'Heureux 2024-01-26 11:42:05 -05:00
• a3a49f39d2
  Updating header in CUB.py Auden Cote-L'Heureux 2024-01-26 11:41:05 -05:00
• f3116ff874
  Updating header in 5b_SummaryStats.py Auden Cote-L'Heureux 2024-01-26 11:40:30 -05:00
• 427f9f7125
  Updating header in 4_CountOGsDiamond.py Auden Cote-L'Heureux 2024-01-26 11:38:42 -05:00
• 887d136f5b
  Updating header in 5a_FinalizeName.py Auden Cote-L'Heureux 2024-01-26 11:37:19 -05:00
• 612e427b4a
  Updating header in 4_CountOGsDiamond.py Auden Cote-L'Heureux 2024-01-26 11:36:32 -05:00
• fa20addc6e
  Updating header in 3_GCodeTranslate.py Auden Cote-L'Heureux 2024-01-26 11:35:25 -05:00
• 7e5e739574
  Updating header in 2_GCodeEval.py Auden Cote-L'Heureux 2024-01-26 11:30:22 -05:00
• 511f0e7766
  Updating header in 1_RenameCDS.py Auden Cote-L'Heureux 2024-01-26 11:26:00 -05:00
• b6954c127a
  Annotating wrapper.py Auden Cote-L'Heureux 2024-01-26 11:17:11 -05:00
• 48c3b08b53
  Updating headers in CUB.py Auden Cote-L'Heureux 2024-01-26 11:07:11 -05:00
• 6a2e815378
  Updating header in 7b_SummaryStats.py Auden Cote-L'Heureux 2024-01-26 11:05:28 -05:00
• 6008160934
  Updating headers in 7a_FinalizeName.py Auden Cote-L'Heureux 2024-01-26 11:01:01 -05:00
• fcd86bfebf
  Updating headers in 6_FilterPartials.py Auden Cote-L'Heureux 2024-01-26 10:43:26 -05:00
• 0167e3da16
  Updating headers in 6_FilterPartials.py Auden Cote-L'Heureux 2024-01-26 10:43:04 -05:00
• a33941b4ed
  Updating headers in 5_GCodeTranslate.py Auden Cote-L'Heureux 2024-01-26 10:39:33 -05:00
• 427f39325b
  Delete Utilities/Basic statistics directory Godwin Ani 2024-01-25 15:17:59 -05:00
• 82de92e12e
  Create Readme.md Godwin Ani 2024-01-25 15:15:50 -05:00
• 59bf186e91
  Small update to concatenate.py Auden Cote-L'Heureux 2024-01-24 11:58:57 -05:00
• 719ce9bb9d
  Added optional line to have keys WITHIN names rather than exclusively at start of name Katzlab 2024-01-20 16:44:02 -05:00
• 3ec22ac4ac
  updating header Katzlab 2024-01-20 16:19:28 -05:00
• 5c6573e0f9
  Updating header Katzlab 2024-01-20 16:18:22 -05:00
• 4b1197eaee
  Headers in 4_InFrameStopCodonEstimator.py Auden Cote-L'Heureux 2024-01-20 13:58:41 -05:00
• 4dd54cf87a
  Headers in 4_InFrameStopCodonEstimator.py Auden Cote-L'Heureux 2024-01-20 13:57:29 -05:00
• 9b02c0074c
  Headers in 3_AssignOGs.py Auden Cote-L'Heureux 2024-01-20 13:50:41 -05:00
• 559eee63f9
  Headers in 3_AssignOGs.py Auden Cote-L'Heureux 2024-01-20 13:49:52 -05:00
• 7268d8f593
  Cluster_v2.0.py Godwin Ani 2024-01-18 09:31:35 -05:00
• e8afd97a16
  Update Cluster_v2.0.py Godwin Ani 2024-01-18 09:29:46 -05:00
• ff9a419c4e
  Updating annotations 2b_Identify_Proks.py Auden Cote-L'Heureux 2024-01-16 14:32:50 -05:00
• c77e63eb74
  Updating header in 2b_Identify_Proks.py Auden Cote-L'Heureux 2024-01-16 14:32:26 -05:00
• e3077b1caa
  Updating header in 2a_Identify_rRNA.py Auden Cote-L'Heureux 2024-01-16 14:10:53 -05:00
• e78d73ca25
  Updating header in 1a_TranscriptLengthFilter.py Auden Cote-L'Heureux 2024-01-16 14:05:44 -05:00
• c15e663773
  Updating header in 1b_CrossPlateContamination.py Auden Cote-L'Heureux 2024-01-16 14:04:06 -05:00
• c12aa46cf5
  Updating header in 1a_TranscriptLengthFilter.py Auden Cote-L'Heureux 2024-01-16 13:53:18 -05:00
• d90e67c266
  Updating header in 2a_Identify_rRNA.py Auden Cote-L'Heureux 2024-01-16 12:11:57 -05:00
• 229bd77cca
  Annotating 1b_CrossPlateContamination.py Auden Cote-L'Heureux 2024-01-16 12:07:32 -05:00
• e9286e7d7a
  Updating header in 1b_CrossPlateContamination.py Auden Cote-L'Heureux 2024-01-16 11:55:23 -05:00
• 1bc56f2a52
  Updating header in 1a_TranscriptLengthFilter.py Auden Cote-L'Heureux 2024-01-16 11:53:01 -05:00
• 3d5cd6cebc
  Updating header in 1a_TranscriptLengthFilter.py Auden Cote-L'Heureux 2024-01-16 11:46:20 -05:00
• 967999ca0d
  Update and rename SeqLengthToCsv_v1.0.py to SeqLenToCsv_v1.0.py Godwin Ani 2024-01-15 15:08:40 -05:00
• 2f6bd2afc5
  Rename PlotComps.r to PlotComps_v2.0.r Godwin Ani 2024-01-15 15:08:03 -05:00
• 14f1caddbc
  Update and rename sharedOGs.py to SharedOGs_v1.0.py Godwin Ani 2024-01-15 15:07:35 -05:00
• 4b4310a0c8
  Update and rename get_taxonomy.py to GetTaxonomy_v1.0.py Godwin Ani 2024-01-15 15:06:34 -05:00