Commits · f14f1db2413a9ee3c9501ade162589e10b3e9b93 · Arendt Group / MorF · GitLab

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Jul 28, 2022
- 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 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
May 16, 2022
- bit score FS overview plots now ordered by median; added aligned plddt~FS score boxplots · 32a913fa
  Nikolaos Papadopoulos authored 2 years ago
  
  32a913fa
May 13, 2022
- added plddt overview · 55296d3a
  Nikolaos Papadopoulos authored 2 years ago
  
  55296d3a
- started making supplemental notebooks, writing main one · 1e98f13d
  Nikolaos Papadopoulos authored 2 years ago
  
  1e98f13d
May 12, 2022
- added more documentation, added structure annot table generation · 6f21bacb
  Nikolaos Papadopoulos authored 2 years ago
  
  6f21bacb
- documented table generation · 390f8c0f
  Nikolaos Papadopoulos authored 2 years ago
  
  390f8c0f
- finalized initial I/O notebook · f6ebcc5e
  Nikolaos Papadopoulos authored 2 years ago
  
  f6ebcc5e
May 09, 2022
- accepted incoming changes · ba9c90ac
  Nikolaos Papadopoulos authored 2 years ago
  
  ba9c90ac
- updated read/write pipeline · 4c1ae0e6
  Nikolaos Papadopoulos authored 2 years ago
  
  4c1ae0e6
May 05, 2022
- UPIMAPI update; confusing but maybe going in the right direction · d19e6f1e
  Fabian Ruperti authored 2 years ago
  
  d19e6f1e
Apr 22, 2022
- Updated README.md so we keep track of contributions · 31dae61d
  Niko Papadopoulos authored 2 years ago
  
  31dae61d
Apr 19, 2022
- updated foldseek search, added sequence information and structure prediction... · b3613054
  Nikolaos Papadopoulos authored 2 years ago
  
  updated foldseek search, added sequence information and structure prediction results as separate tables
  b3613054
Apr 13, 2022
- single cell analysis now ready · 3a041ff3
  Nikolaos Papadopoulos authored 2 years ago
  
  3a041ff3