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aging-research
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species

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  1. select_genes:
    2. 

  2.   cmd: papermill -f stages/1_select_genes_and_species.yaml  --progress-bar --report-mode
    3. 

  3.     notebooks/1_select_genes_and_species.ipynb data/output/notebooks/1_select_genes_and_species_report.ipynb
    4. 

  4.   deps:
    5. 

  5.   - path: data/input/genes/by_animal_class
    6. 

  6.     md5: 5bb1b3db720c77cb0800fa40f0196f29.dir
    7. 

  7.   - path: data/input/samples.tsv
    8. 

  8.     md5: 17e2bb8020c8ac1f8c3c7445fac901c3
    9. 

  9.   - path: data/input/species.tsv
    10. 

  10.     md5: cdf6379f1d78780afc6f650b10636494
    11. 

  11.   - path: notebooks/1_select_genes_and_species.ipynb
    12. 

  12.     md5: 201de29fbe33b8bf5b546fcf16ec15f6
    13. 

  13.   - path: stages/1_select_genes_and_species.yaml
    14. 

  14.     md5: 22f95cba7413c7c641fec0720b8338ee
    15. 

  15.   outs:
    16. 

  16.   - path: data/interim/selected_expressions.tsv
    17. 

  17.     md5: d872ec9f5ff9ac16d7dd6d877cc077b1
    18. 

  18.   - path: data/interim/selected_genes.tsv
    19. 

  19.     md5: dc2b3b921d9fb4ed358a085c53426307
    20. 

  20.   - path: data/interim/selected_samples.tsv
    21. 

  21.     md5: f3a11a4ad6550a7f356bf51e7a4e183b
    22. 

  22.   - path: data/interim/selected_species.tsv
    23. 

  23.     md5: 74a64f77b443ed7b6e9b44240953ec7a
    24. 

  24.   - path: data/output/counts/species_sample_count.tsv
    25. 

  25.     md5: eced40b842c0ec786a43d0e8c1da073d
    26. 

  26.   - path: data/output/counts/species_tissue_sample_count.tsv
    27. 

  27.     md5: 7e78391b84b265bdc0db65ef0f293056
    28. 

  28.   - path: data/output/counts/tissue_sample_count.tsv
    29. 

  29.     md5: 95d7d50886117aae30a8ee8c335f5076
    30. 

  30.   - path: data/output/notebooks/1_select_genes_and_species_report.ipynb
    31. 

  31.     md5: c170a67d0a586c49d1442695c78bdcbc
    32. 

  32. select_samples:
    33. 

  33.   cmd: papermill -f parameters/select_samples.yaml  --progress-bar --report-mode notebooks/select_samples.ipynb
    34. 

  34.     data/output/notebooks/select_samples.ipynb
    35. 

  35.   deps:
    36. 

  36.   - path: data/input/genes/by_animal_class
    37. 

  37.     md5: 5bb1b3db720c77cb0800fa40f0196f29.dir
    38. 

  38.   - path: data/input/samples.tsv
    39. 

  39.     md5: 17e2bb8020c8ac1f8c3c7445fac901c3
    40. 

  40.   - path: data/input/species.tsv
    41. 

  41.     md5: cdf6379f1d78780afc6f650b10636494
    42. 

  42.   - path: data/input/total_mtDNA_base_composition.csv
    43. 

  43.     md5: 3735cfc4beffb6c9356f908525345ee6
    44. 

  44.   - path: notebooks/select_samples.ipynb
    45. 

  45.     md5: 246a58020b01860eb71cdb558b28bac0
    46. 

  46.   - path: parameters/select_samples.yaml
    47. 

  47.     md5: aa126cb70666d7352f7e6ff6005124b7
    48. 

  48.   outs:
    49. 

  49.   - path: data/interim/selected/expressions.tsv
    50. 

  50.     md5: 60942869bc29257f57b92088337922b0
    51. 

  51.   - path: data/interim/selected/genes.tsv
    52. 

  52.     md5: 08f457c2517b3f601f5e58e3b1ec4ae0
    53. 

  53.   - path: data/interim/selected/genes_meta.tsv
    54. 

  54.     md5: 0387f21fcd4b287dc924432c8b90042d
    55. 

  55.   - path: data/interim/selected/samples.tsv
    56. 

  56.     md5: c370e925f56a0ed33b7dcb16553d4c39
    57. 

  57.   - path: data/interim/selected/species.tsv
    58. 

  58.     md5: 44e0c63a0d7749abcd43b3c1f92cc54b
    59. 

  59.   - path: data/output/counts/species_sample_count.tsv
    60. 

  60.     md5: eced40b842c0ec786a43d0e8c1da073d
    61. 

  61.   - path: data/output/counts/species_tissue_sample_count.tsv
    62. 

  62.     md5: 7e78391b84b265bdc0db65ef0f293056
    63. 

  63.   - path: data/output/counts/tissue_sample_count.tsv
    64. 

  64.     md5: 95d7d50886117aae30a8ee8c335f5076
    65. 

  65.   - path: data/output/notebooks/select_samples.ipynb
    66. 

  66.     md5: 954d63d340cf17a15c9cc5235839c7cd
    67. 

  67. results_intersections:
    68. 

  68.   cmd: papermill -f parameters/results_intersections.yaml  --progress-bar --report-mode
    69. 

  69.     notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
    70. 

  70.   deps:
    71. 

  71.   - path: data/output/external/causality
    72. 

  72.     md5: c00e3428ab5aac19fdc6c5157b09fb33.dir
    73. 

  73.   - path: data/output/external/causality/causal_relations_5_tissues_anton_species_5_bootstraps.csv
    74. 

  74.     md5: e3cf4199fa5234888c6fe0f388f87426
    75. 

  75.   - path: data/output/external/linear
    76. 

  76.     md5: ccaa8c167006ee5e320c709bfcdc0d6d.dir
    77. 

  77.   - path: data/output/external/shap
    78. 

  78.     md5: fb35c5a65c49be61d7dacdc1fba3764b.dir
    79. 

  79.   outs:
    80. 

  80.   - path: data/output/intersections/genage_human_intersections.tsv
    81. 

  81.     md5: 7cd1e7ff10c8e35b41e884f355911437
    82. 

  82.   - path: data/output/intersections/genage_model_intersections.tsv
    83. 

  83.     md5: adaefd5646ae0c275ec680989663ef9c
    84. 

  84.   - path: data/output/intersections/intersections.tsv
    85. 

  85.     md5: d9748c0547ec3c01f122c2a967e6d37e
    86. 

  86.   - path: data/output/intersections/intersections_5_and_7.tsv
    87. 

  87.     md5: 5606ff2b9dd0269104b07509760fb824
    88. 

  88.   - path: data/output/intersections/new_old_comparison.tsv
    89. 

  89.     md5: 440391dfccd04e58897f3bb1c898b74b
    90. 

  90.   - path: data/output/notebooks/results_intersections.ipynb
    91. 

  91.     md5: 4aa03ee3831120e7a7d76ed0351e9a46
    92. 

  92. shap_selection:
    93. 

  93.   cmd: papermill -f parameters/shap_selection.yaml  --progress-bar --report-mode notebooks/shap_selection.ipynb
    94. 

  94.     data/output/notebooks/shap_selection.ipynb
    95. 

  95.   deps:
    96. 

  96.   - path: data/interim/selected/expressions.tsv
    97. 

  97.     md5: 60942869bc29257f57b92088337922b0
    98. 

  98.   - path: data/interim/selected/genes.tsv
    99. 

  99.     md5: 08f457c2517b3f601f5e58e3b1ec4ae0
    100. 

  100.   - path: data/interim/selected/genes_meta.tsv
    101. 

  101.     md5: 0387f21fcd4b287dc924432c8b90042d
    102. 

  102.   - path: data/interim/selected/samples.tsv
    103. 

  103.     md5: c370e925f56a0ed33b7dcb16553d4c39
    104. 

  104.   - path: data/interim/selected/species.tsv
    105. 

  105.     md5: 44e0c63a0d7749abcd43b3c1f92cc54b
    106. 

  106.   outs:
    107. 

  107.   - path: data/output/notebooks/shap_selection.ipynb
    108. 

  108.     md5: 42a09aec93f5f95dad8105eb9c98e077
    109.
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Integrate Google Cloud Storage
Use Google Storage
Select bucket
Upload key
Finish

Use Google Cloud Storage!

Browsing data directories saved to Google Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Google Storage bucket

Service Account Key

Congratulations!

species is now integrated with Google Cloud Storage!

Delete Storage Key

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No
Yes
Integrate AWS S3
Use S3 remote
Select bucket
Access key
Finish

Use AWS S3 as storage!

Browsing data directories saved to S3 is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your S3 bucket

Access key (If needed)

Congratulations!

species is now integrated with AWS S3!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes
Integrate S3 compatible storage
Use S3 like remote
Select bucket
Access key
Finish

Use any S3 compatible storage!

Browsing data directories saved to S3 compatible storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your S3 bucket

Access key (If needed)

Congratulations!

species is now integrated with your S3 compatible storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes
Integrate Azure Cloud Storage
Use Azure Storage
Select bucket
Set key
Finish

Use Azure Cloud Storage!

Browsing data directories saved to Azure Cloud Storage is possible with DAGsHub. Let's configure your repository to easily display your data in the context of any commit!

Specify your Azure Storage bucket

Access key (If needed)

Congratulations!

species is now integrated with Azure Cloud Storage!

Delete Storage Key

Are you sure you want to delete this access key?

No
Yes