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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: 553087164c9551c61bba6a9be28922d2
    46. 

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

  47.     md5: ccd2ff9e431a861a3cabaf02eb5533ab
    48. 

  48.   outs:
    49. 

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

  50.     md5: ea8b027a11acb7da8223ed2ed4761509
    51. 

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

  52.     md5: f410753d92961599f8da2370c6e25f42
    53. 

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

  54.     md5: cb271541402f3e1f66de865dce6c49ea
    55. 

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

  56.     md5: 9812c3858cb3e1c524a19713aff488fe
    57. 

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

  58.     md5: 31ac984b2cb60c082f8023759a30d033
    59. 

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

  60.     md5: 84c76b86cb61c5bf73c7f06c390dc064
    61. 

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

  62.     md5: e1b7a7f290203cad12f412d33e2a0bcb
    63. 

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

  64.     md5: 5a1441ea61f14d0242037f6a36c9d4a4
    65. 

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

  66.     md5: 62b9af37d4b5f0a9b2399652594b021b
    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.   - path: parameters/results_intersections.yaml
    80. 

  80.     md5: b1f4e5899bf2548de8a69cb96ce6f192
    81. 

  81.   outs:
    82. 

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

  83.     md5: 7cd1e7ff10c8e35b41e884f355911437
    84. 

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

  85.     md5: adaefd5646ae0c275ec680989663ef9c
    86. 

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

  87.     md5: d9748c0547ec3c01f122c2a967e6d37e
    88. 

  88.   - path: data/output/intersections/intersections_5_and_7.tsv
    89. 

  89.     md5: 5606ff2b9dd0269104b07509760fb824
    90. 

  90.   - path: data/output/intersections/new_old_comparison.tsv
    91. 

  91.     md5: 440391dfccd04e58897f3bb1c898b74b
    92. 

  92.   - path: data/output/notebooks/results_intersections.ipynb
    93. 

  93.     md5: 4aa03ee3831120e7a7d76ed0351e9a46
    94. 

  94. shap_selection:
    95. 

  95.   cmd: papermill -f parameters/shap_selection.yaml  --progress-bar --report-mode notebooks/shap_selection.ipynb
    96. 

  96.     data/output/notebooks/shap_selection.ipynb
    97. 

  97.   deps:
    98. 

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

  99.     md5: ea8b027a11acb7da8223ed2ed4761509
    100. 

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

  101.     md5: f410753d92961599f8da2370c6e25f42
    102. 

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

  103.     md5: cb271541402f3e1f66de865dce6c49ea
    104. 

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

  105.     md5: 9812c3858cb3e1c524a19713aff488fe
    106. 

  106.   - path: data/interim/selected/species.tsv
    107. 

  107.     md5: 31ac984b2cb60c082f8023759a30d033
    108. 

  108.   - path: parameters/shap_selection.yaml
    109. 

  109.     md5: 43734a0f6f4865a78d36e5ea7e773176
    110. 

  110.   outs:
    111. 

  111.   - path: data/output/notebooks/shap_selection.ipynb
    112. 

  112.     md5: c48cb96cd95b4936a3adb043018a6d8c
    113. 

  113. tuning:
    114. 

  114.   cmd: echo "work in progress!"
    115. 

  115.   deps:
    116. 

  116.   - path: data/interim/selected/expressions.tsv
    117. 

  117.     md5: e8e8ea38f54eec4c9d51069d8cc2fde0
    118. 

  118.   - path: data/interim/selected/genes.tsv
    119. 

  119.     md5: 08f457c2517b3f601f5e58e3b1ec4ae0
    120. 

  120.   - path: data/interim/selected/genes_meta.tsv
    121. 

  121.     md5: 0387f21fcd4b287dc924432c8b90042d
    122. 

  122.   - path: data/interim/selected/samples.tsv
    123. 

  123.     md5: c370e925f56a0ed33b7dcb16553d4c39
    124. 

  124.   - path: data/interim/selected/species.tsv
    125. 

  125.     md5: 44e0c63a0d7749abcd43b3c1f92cc54b
    126. 

  126.   outs:
    127. 

  127.   - path: data/output/optimization/study.sqlite
    128. 

  128.     md5: ef8116b0684832e6e11749edcd4e5cbf
    129. 

  129. tune:
    130. 

  130.   cmd: python tune.py
    131. 

  131.   deps:
    132. 

  132.   - path: data/interim/selected/expressions.tsv
    133. 

  133.     md5: ea8b027a11acb7da8223ed2ed4761509
    134. 

  134.   - path: data/interim/selected/genes.tsv
    135. 

  135.     md5: f410753d92961599f8da2370c6e25f42
    136. 

  136.   - path: data/interim/selected/genes_meta.tsv
    137. 

  137.     md5: cb271541402f3e1f66de865dce6c49ea
    138. 

  138.   - path: data/interim/selected/samples.tsv
    139. 

  139.     md5: 9812c3858cb3e1c524a19713aff488fe
    140. 

  140.   - path: data/interim/selected/species.tsv
    141. 

  141.     md5: 31ac984b2cb60c082f8023759a30d033
    142. 

  142.   params:
    143. 

  143.     parameters/tune.yaml:
    144. 

  144.       folds: 5
    145. 

  145.       hold_outs: 1
    146. 

  146.       name: general_tuner
    147. 

  147.       not_validated_species: ''
    148. 

  148.       repeats: 10
    149. 

  149.       species_in_validation: 3
    150. 

  150.       threads: 1
    151. 

  151.       trials: 10
    152. 

  152.   outs:
    153. 

  153.   - path: data/metrics/lifespan/metrics.csv
    154. 

  154.     md5: 79b0c703e95be0e1eba09b8179f9b032
    155. 

  155.   - path: data/metrics/lifespan/parameters.json
    156. 

  156.     md5: 39716c866e5d47b2a912cb022acfccf0
    157. 

  157.   - path: data/metrics/lifespan/study.sqlite
    158. 

  158.     md5: c21ce7d1ce5f5fb3074138834691c366
    159.
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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

Are you sure you want to delete this access key?

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