Commits · 0edb1ccec67e8d694ae5d1f2d860c66bf405c9db · Arendt Group / MorF

Jun 17, 2022

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 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
- updated foldseek search to include low-confidence hits; revamping analysis to... · 6ca4b802
  Nikolaos Papadopoulos authored 2 years ago
  
  updated foldseek search to include low-confidence hits; revamping analysis to separate preprocessing from plotting (but plots still in there, they are so nice)
  6ca4b802
Apr 12, 2022
- added sequence annotation column to spongilla; some additional plots · 6a43c301
  Fabian Ruperti authored 2 years ago
  
  6a43c301
- Merge branch 'main' of https://git.embl.de/grp-arendt/spongfold into main · ff99b654
  Fabian Ruperti authored 2 years ago
  
  ff99b654
- added sequence annotation column to spongilla; some additional plots · 53085051
  Fabian Ruperti authored 2 years ago
  
  53085051
- Merge branch 'ruperti-main-patch-43727' into 'main' · 5e7f1b5d
  Niko Papadopoulos authored 2 years ago
  
  Update README.md See merge request grp-arendt/spongfold!1
  5e7f1b5d
Apr 11, 2022
- added sequence annotation column to spongilla dataframe; tried some plots · b2857ae1
  Fabian Ruperti authored 2 years ago
  
  b2857ae1
- mapped PDB IDs to UniProt, updated EggNOG input parsing · b0737a3b
  Nikolaos Papadopoulos authored 2 years ago
  
  b0737a3b
- added new emapper run; successful colabfold script · 1d063cd8
  Nikolaos Papadopoulos authored 2 years ago
  
  1d063cd8
Apr 04, 2022
- first analysis with Fabi · bafee417
  Nikolaos Papadopoulos authored 2 years ago
  
  bafee417
- batch1 run finished; setting up analysis · 91c6e2b0
  Nikolaos Papadopoulos authored 2 years ago
  
  91c6e2b0
Apr 01, 2022
- scripts to run MSAs finalized; tri trialled alphafold prediction; started big run · bbd82d82
  Nikolaos Papadopoulos authored 2 years ago
  
  bbd82d82
Mar 25, 2022
- fixed load and run requirements for colabfold_search · d4d1a2ed
  Nikolaos Papadopoulos authored 3 years ago
  
  d4d1a2ed
Mar 22, 2022
- installed colabfold dependencies, trying to run · ce6a741e
  Nikolaos Papadopoulos authored 3 years ago
  
  ce6a741e
Mar 16, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/spongfold into main · 5044660b
  Nikolaos Papadopoulos authored 3 years ago
  
  5044660b
- sequence alignments vs UniRef30, PDB · c63c7b63
  Nikolaos Papadopoulos authored 3 years ago
  
  c63c7b63
Mar 15, 2022
- Update README.md · 49dcc056
  Fabian Ruperti authored 3 years ago
  
  49dcc056