1. 18 Nov, 2022 1 commit
  2. 30 Sep, 2022 2 commits
  3. 01 Aug, 2022 2 commits
  4. 31 Jul, 2022 1 commit
  5. 28 Jul, 2022 2 commits
  6. 26 Jul, 2022 1 commit
  7. 25 Jul, 2022 1 commit
  8. 22 Jul, 2022 2 commits
    • Cecilia SENSALARI's avatar
      Small changes to handle the actual clade · fb9b2fdf
      Cecilia SENSALARI authored
      - I was so far using mock species, but now
        that I've generated the file I needed
        (results from OrthoFinder where the fagales
        clade was added altogether to update the
        37-species orthogroups) I can use the
        actual name of the fagales species in the clade
      fb9b2fdf
    • Cecilia SENSALARI's avatar
      Get gene count of clade species altogether · 81710766
      Cecilia SENSALARI authored
      - New strategy: the small calde is added
        to the 37-orthofinder results altogether
      - This new code parses the resulting OF
        orthogroups and 1) gets the equivalent
        of the original top 100 orthogroups; 2)
        gets those which at least one clade
        species has genes.
      - Finally computes and outputs the gene
        counts for such families for the whole
        clade in a tab-seprataed DataFrame
      81710766
  9. 20 Jul, 2022 1 commit
  10. 14 Jul, 2022 1 commit
    • Cecilia SENSALARI's avatar
      Merge GFs and generate gene counts · 21d1701e
      Cecilia SENSALARI authored
      - When original GF hits two OrthoFinder GFs,
        these two latter ones are merged and they
        are called with sorted label "GF1_GF2"
      
      - Gene counts are printed to file with GF
        as index labels; GFs are sorted by
        descending gene count
      21d1701e
  11. 28 Jun, 2022 2 commits
  12. 14 Jun, 2022 2 commits
  13. 08 Jun, 2022 1 commit
    • Cecilia SENSALARI's avatar
      Integration of OrthoFinder in ksrates · fadb3fa9
      Cecilia SENSALARI authored
      - finally included cucumis melo and hordeum
        vulgare, so that I now have all the 37
        angiosperm species that were used in the past
        for the rec.ret. gene families
      - ksrates code and main.nf run OrthoFinder
        from within the ksrates code
      - ksrates also runs the analysis to find the top
        e.g. 2000 reciprocally retained gene families
        among the thosands of OrthoFinder orthogroups
      fadb3fa9
  14. 27 May, 2022 1 commit
  15. 17 May, 2022 1 commit
  16. 06 May, 2022 1 commit
  17. 05 May, 2022 1 commit
  18. 03 May, 2022 1 commit
    • Cecilia SENSALARI's avatar
      Add options (any extra genes, test_run): · 013f6eb4
      Cecilia SENSALARI authored
      - Allow accepting any OF orthogroup even if
        it contains many extra non-top genes.
      - set option "test_run" to avoid generating
        files with incomplete data
      - Generate filename variables
      013f6eb4
  19. 29 Apr, 2022 1 commit
    • Cecilia SENSALARI's avatar
      ADD ORTHOFINDER [WIP] instead of DIAMOND · 9ea5eb87
      Cecilia SENSALARI authored
      - For testing purposes, added switch parameter
        to switch between diamond and orthofinder.
      - orthofinder itself is not yet run by ksrates
        because of dependency issues (diamond not
        found!). But the analysis of orthofinder
        results is performed to find the top 2000
        gene families in the OF orthogroups.
      - Continues with classic Ks estimate and plots.
      9ea5eb87
  20. 29 Mar, 2022 4 commits
  21. 02 Mar, 2022 2 commits
  22. 03 Feb, 2022 2 commits
  23. 02 Feb, 2022 2 commits
  24. 25 Jan, 2022 2 commits
  25. 24 Dec, 2021 2 commits
  26. 07 Dec, 2021 1 commit