Commits · bbda981af91b315cd0916cb8e8a8ad171c387577 · Arendt Group / MorF · GitLab

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Sep 01, 2022
- added model species foldseek searches · bbda981a
  nikolaos.papadopoulos@embl.de authored 2 years ago
  
  bbda981a
Aug 17, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/CoFFE into main · 711581d3
  Nikolaos Papadopoulos authored 2 years ago
  
  711581d3
- fixed ModelArchive bugs (protein names/models, protein query length); added... · 9d321e6a
  Nikolaos Papadopoulos authored 2 years ago
  
  fixed ModelArchive bugs (protein names/models, protein query length); added AFDB self comparison as per editors' request
  9d321e6a
Aug 02, 2022
- reworking analysis to accommodate new UniProt RESTful API · e0fada09
  Nikolaos Papadopoulos authored 2 years ago
  
  e0fada09
- updated README with aims, license · 59641e28
  Niko Papadopoulos authored 2 years ago
  
  v1.0
  
  59641e28
- update scripts to new paths, new conda env name · 9e154601
  Niko Papadopoulos authored 2 years ago
  
  9e154601
- Add LICENSE · ee0e19cf
  Niko Papadopoulos authored 2 years ago
  
  ee0e19cf
Aug 01, 2022
- now manual workaround for PDB ID mapping · 5276fe26
  Nikolaos Papadopoulos authored 2 years ago
  
  5276fe26
Jul 29, 2022
- temp saving of AFDB, SWP parquets now possible; minor file structure changes · 8dd17e2e
  Nikolaos Papadopoulos authored 2 years ago
  
  8dd17e2e
Jul 28, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/CoFFE into main · 6a5ed0e3
  Nikolaos Papadopoulos authored 2 years ago
  
  6a5ed0e3
- migrating read/write to scripts and out of notebook · f14f1db2
  Nikolaos Papadopoulos authored 2 years ago
  
  f14f1db2
- Add scripts to reproduce the sequence and profile search based analysis · 62a76855
  Milot Mirdita authored 2 years ago
  
  62a76855
Jul 15, 2022
- Merge branch 'npapadop-main-patch-23276' into 'main' · abf52890
  Niko Papadopoulos authored 2 years ago
  
  updated README to reflect the stage of the project See merge request grp-arendt/CoFFE!2
  abf52890
- updated README to reflect the stage of the project · fb68c6cc
  Niko Papadopoulos authored 2 years ago
  
  fb68c6cc
Jul 13, 2022
- cleanup and preparation for submission · e619cd50
  Nikolaos Papadopoulos authored 2 years ago
  
  e619cd50
Jul 12, 2022
- staging for submission · 1c4a5e31
  Nikolaos Papadopoulos authored 2 years ago
  
  1c4a5e31
Jul 07, 2022
- merged conflicts in DEG revisited · d4323513
  Nikolaos Papadopoulos authored 2 years ago
  
  d4323513
- rerunning scripts for plots · b261f98e
  Nikolaos Papadopoulos authored 2 years ago
  
  b261f98e
Jul 06, 2022
- update annotation_categories for suppl fig 2.1, 2.2 and 2.3 · bb34d6e7
  Fabian Ruperti authored 2 years ago
  
  bb34d6e7
- updated suppl-annotaion-categories to make suppl fig 2.1 and 2.2 · 76394efc
  Fabian Ruperti authored 2 years ago
  
  76394efc
- added suppl-mesocytes, including the supplemental figure mesocyte dotplot · 2088fbcf
  Fabian Ruperti authored 2 years ago
  
  2088fbcf
Jul 01, 2022
- update of pinacocyte story · feb1babb
  Fabian Ruperti authored 2 years ago
  
  feb1babb
Jun 29, 2022
- added CAI calculation to horizontal gene transfer, theory from Degnan review · 89dea862
  Nikolaos Papadopoulos authored 2 years ago
  
  89dea862
Jun 28, 2022
- updated gene lists for pinacocyte dotplots · 2f852964
  Nikolaos Papadopoulos authored 2 years ago
  
  2f852964
- minor plotting changes in analysis, added pinacocyte dotplot creation · 9763b5f6
  Nikolaos Papadopoulos authored 2 years ago
  
  9763b5f6
Jun 17, 2022
- was overeager during merging, restoring databases_pdb · d71d75fa
  Nikolaos Papadopoulos authored 2 years ago
  
  d71d75fa
- merged · 2fd10229
  Nikolaos Papadopoulos authored 2 years ago
  
  2fd10229
- added countland inspection of single cell; looked at evidence for HGT;... · 0edb1cce
  Nikolaos Papadopoulos authored 2 years ago
  
  added countland inspection of single cell; looked at evidence for HGT; included Fabi's exploration of various protein characteristics in relation to annotation status
  0edb1cce
Jun 15, 2022

script cleanup · 8299e04d

Niko Papadopoulos authored 2 years ago

- moved to scripts folder
- wrote README
- removed obsolete
- renamed properly

8299e04d

Jun 13, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/spongfold into main · 8bc04a68
  Nikolaos Papadopoulos authored 2 years ago
  
  8bc04a68
- quality control on the way to submission · 4742560d
  Nikolaos Papadopoulos authored 2 years ago
  
  4742560d
May 30, 2022
- uncommented UniRef30 index calc · 35d77e8c
  Niko Papadopoulos authored 2 years ago
  
  35d77e8c
May 25, 2022
- z score analysis of where DEGs come from · 5a0c77c0
  Nikolaos Papadopoulos authored 2 years ago
  
  5a0c77c0
May 23, 2022
- replacing single-cell analysis with DEG analysis · 6b6e7cbf
  Nikolaos Papadopoulos authored 2 years ago
  
  6b6e7cbf
May 20, 2022
- updated analysis · 193c22b5
  Nikolaos Papadopoulos authored 2 years ago
  
  193c22b5
May 19, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/spongfold into main · 932599f8
  Nikolaos Papadopoulos authored 2 years ago
  
  932599f8
- moved analysis to the point of the single cell; added Fabi's proteomics data · 3abc50f7
  Nikolaos Papadopoulos authored 2 years ago
  
  3abc50f7
May 18, 2022
- comparison of annotation categories for plddt, MSA size, physico chemical parameters · 7694fae9
  Fabian Ruperti authored 2 years ago
  
  7694fae9
May 17, 2022
- colors are now consistent · bbc44c85
  Nikolaos Papadopoulos authored 2 years ago
  
  bbc44c85
- going deeper on the structure/sequence annotation comparison · a26015c0
  Nikolaos Papadopoulos authored 2 years ago
  
  a26015c0