Commits · main · Arendt Group / MorF

Mar 27, 2023
- updated to now save morpholog tables · ccba7188
  Niko Papadopoulos authored 1 year ago
  
  v1.2
  
  ccba7188
Jan 25, 2023
- now running MMseqs2 with -s 7 · 32da861d
  Niko Papadopoulos authored 2 years ago
  
  v1.1
  
  32da861d
- revisit MorF-EggNOG overlap (Table 3) · 30b67fc7
  Niko Papadopoulos authored 2 years ago
  
  30b67fc7
Jan 24, 2023
- looked at EC of second-best morphologs and why they sometimes disagree; looked... · c29d13de
  Niko Papadopoulos authored 2 years ago
  
  looked at EC of second-best morphologs and why they sometimes disagree; looked at available choanos for HGT candidates
  c29d13de
Jan 12, 2023
- finally removing Untitled.ipynb · 7450654c
  Niko Papadopoulos authored 2 years ago
  
  7450654c
- removed image · cef41e2a
  Niko Papadopoulos authored 2 years ago
  
  cef41e2a
- added HMMER annotation performance · 7c3fa17d
  Niko Papadopoulos authored 2 years ago
  
  7c3fa17d
Jan 09, 2023
- added HMMER analysis, morpholog phylogenetic distribution, and additional info on table3 · 7f88d077
  Niko Papadopoulos authored 2 years ago
  
  7f88d077
Dec 28, 2022
- rerun to produce figures · e71eca47
  Niko Papadopoulos authored 2 years ago
  
  e71eca47
Dec 21, 2022
- fixed EC calculation for remote species; answered top N morpholog question. · 78a6b710
  Niko Papadopoulos authored 2 years ago
  
  78a6b710
Dec 20, 2022
- comparison of top N hits at certain score margin done; discovered bug with EC comparison · 3047dac4
  Niko Papadopoulos authored 2 years ago
  
  3047dac4
- how well is protein function captured by the top morphologs? · d9c064b8
  Niko Papadopoulos authored 2 years ago
  
  d9c064b8
- update GO analysis with GO depth · ed65d494
  Fabian Ruperti authored 2 years ago
  
  ed65d494
Dec 16, 2022
- GO term comparison notebook finished · 62ebdb07
  Fabian Ruperti authored 2 years ago
  
  62ebdb07
- renaming revision notebooks; added yeast/arabidopsis-human comparison · bc9cc294
  Niko Papadopoulos authored 2 years ago
  
  bc9cc294
Dec 15, 2022
- revision GO term comparison · 97404076
  Fabian Ruperti authored 2 years ago
  
  97404076
- added statistical comparison of avg pLDDT distributions · 2c08e415
  Niko Papadopoulos authored 2 years ago
  
  2c08e415
Sep 01, 2022
- added model species foldseek searches · bbda981a
  nikolaos.papadopoulos@embl.de authored 2 years ago
  
  bbda981a
Aug 17, 2022
- 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
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
- migrating read/write to scripts and out of notebook · f14f1db2
  Nikolaos Papadopoulos authored 2 years ago
  
  f14f1db2
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
- 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

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
- quality control on the way to submission · 4742560d
  Nikolaos Papadopoulos authored 2 years ago
  
  4742560d
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
- 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