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annotation.rst

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  1. Analysis/Annotation
    2. 

  2. ===================
    3. 

  3. 

  4. Tripal Analysis Expression
    5. 

  5. --------------------------
    6. 

  6. 

  7. A module for loading, annotating, and visualizing NCBI Biosamples and expression data.
    8. 

  8. 

  9. `Documentation <https://github.com/tripal/tripal_analysis_expression/blob/master/README.md>`__
    10. 

  10. `Repository <https://github.com/tripal/tripal_analysis_expression>`__
    11. 

  11. 

  12. Tripal Analysis Blast
    13. 

  13. ---------------------
    14. 

  14. 

  15. This module extends the Tripal Analysis Module and provides a method for loading XML results from the NCBI blast program. Blast results appear on each feature page.
    16. 

  16. 

  17. `Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/blast.html>`__
    18. 

  18. `Repository <https://github.com/tripal/tripal_analysis_blast>`__
    19. 

  19. 

  20. Tripal Analysis KEGG
    21. 

  21. --------------------
    22. 

  22. 

  23. This module provides a method for loading of KEGG ortholog assignments derived from the KEGG Automated Annotation Server (KAAS). KEGG assignments appear on each feature page, and a full KEGG report is available for browsing results once uploaded.
    24. 

  24. 

  25. `Repository <https://github.com/tripal/tripal_analysis_kegg>`__
    26. 

  26. 

  27. Tripal Analysis Interpro
    28. 

  28. ------------------------
    29. 

  29. 

  30. This module provides a method for loading XML results from the InterProScan program. The module can load InterProScan XML v4 or InterProScan XML v5 generated from the command-line or web-based versions of InterProScan. Additionally, GO terms mapped by InterProScan can optionally be assigned to features.
    31. 

  31. 

  32. `Documentation <https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/func_annots/interpro.html>`__
    33. 

  33. `Repository <https://github.com/tripal/tripal_analysis_interpro>`__
    34. 

  34. 

  35. Tripal JBrowse
    36. 

  36. --------------
    37. 

  37. 

  38. This module provides integration between Tripal sites and pre-existing GMOD JBrowse instances. It allows you to create pages on your Tripal site with an embedded JBrowse instance by filling out a simple form.
    39. 

  39. 

  40. `Documentation <https://github.com/tripal/tripal_jbrowse/blob/7.x-2.1.x/README.md>`__
    41. 

  41. `Repository <https://github.com/tripal/tripal_jbrowse>`__
    42. 

  42. 

  43. Tripal CV-Xray
    44. 

  44. --------------
    45. 

  45. 

  46. Tripal CV-Xray maps content annotations onto controlled vocabulary trees.  The end result is a browseable CV field that lets users explore ontologies and find associated content.
    47. 

  47. 

  48. `Documentation <https://github.com/statonlab/tripal_cv_xray/blob/master/README.md>`__
    49. 

  49. `Repository <https://github.com/statonlab/tripal_cv_xray>`__
    50. 

  50. 

  51. Tripal Galaxy
    52. 

  52. -------------
    53. 

  53. 

  54. This module is for integration of Tripal and the Galaxy Project. It facillitates the creation of forms on your Tripal site that submit jobs to a galaxy instance.
    55. 

  55. 

  56. `Documentation <https://github.com/tripal/tripal_galaxy/blob/7.x-1.x/README.md>`__
    57. 

  57. `Repository <https://github.com/tripal/tripal_galaxy>`__
    58.