1. 02 Jul, 2019 1 commit
  2. 27 Jun, 2019 1 commit
  3. 21 Jun, 2019 2 commits
    • domingue's avatar
      Fixed issue related to missing gene names in more standard gtf annotations.... · 2315be90
      domingue authored
      Fixed issue related to missing gene names in more standard gtf annotations. Tested with Homo sapiens (Ensembl_v88_custom, GRCh38).
      2315be90
    • domingue's avatar
      Addresses issue #57. A GTF option has been included and now all gene... · 294dc4fd
      domingue authored
      Addresses issue #57. A GTF option has been included and now all gene information is extracted with the following hierarchy: GTF, gene_info table, biomaRT.
      It also uses the non-redundant exonic length (effective gene length) to calculate RPKMs and TPMs. If the GTF is not present it reverts to the old method.
      
      Tested with a planaria GTF, which does not contain gene names or any other information apart from ensembl_gene_id and transctipt_id. It might be good to test with a human / mouse GTF.
      
      TODO or at least to consider: (i) add GTF as a mandatory argument; (ii) use bioMart as a backup to find gene names and description if not present in the GTF (use case would some weird GTFs).
      294dc4fd
  4. 18 Jun, 2019 1 commit
  5. 17 Jun, 2019 1 commit
  6. 11 Jun, 2019 1 commit
  7. 07 Jun, 2019 1 commit
  8. 10 May, 2019 1 commit
  9. 24 Apr, 2019 1 commit
  10. 04 Apr, 2019 1 commit
  11. 13 Mar, 2019 1 commit
  12. 11 Feb, 2019 2 commits
  13. 29 Jan, 2019 2 commits
  14. 22 Jan, 2019 1 commit
  15. 14 Dec, 2018 2 commits
  16. 15 Nov, 2018 3 commits
  17. 07 Nov, 2018 1 commit
  18. 02 Nov, 2018 1 commit
  19. 30 Oct, 2018 1 commit
  20. 19 Oct, 2018 1 commit
  21. 19 Sep, 2018 1 commit
  22. 30 Aug, 2018 2 commits
  23. 16 Aug, 2018 3 commits
  24. 06 Jul, 2018 1 commit
  25. 26 Jun, 2018 1 commit
  26. 20 Jun, 2018 1 commit
  27. 25 May, 2018 2 commits
  28. 03 May, 2018 2 commits
  29. 02 May, 2018 1 commit