deeprofiler project processing features

d33bs · Jan 17, 2023 · 3137e54 · 3137e54
1 parent 1ae36c3
commit 3137e54
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Showing 12 changed files with 2,557 additions and 3 deletions.
diff --git a/4_processing_features/4.extract_sc_features.sh b/4_processing_features/4.extract_sc_features.sh
@@ -1,3 +1,6 @@
 #!/bin/bash
-jupyter nbconvert --to python extract_single_cell_features.ipynb
-python extract_single_cell_features.py
+jupyter nbconvert --to python extract_sc_features_cp.ipynb
+python extract_sc_features_cp.py
+
+jupyter nbconvert --to python extract_sc_features_dp.ipynb
+python extract_sc_features_dp.py
diff --git a/4_processing_features/4.processing_features.yml b/4_processing_features/4.processing_features.yml
@@ -14,4 +14,4 @@ dependencies:
   - conda-forge::numpy=1.22
   - conda-forge::scikit-learn
   - pip:
-    - git+https://github.com/cytomining/pycytominer@e43be528d3ca6d77d2b1a347fe8e4131dfc65bf0
+    - git+https://github.com/cytomining/pycytominer@afac3ea16818ad25f37318ecd5c5090c0eff5806
diff --git a/4_processing_features/data/nf1_sc_deepprofiler_cyto.csv.gz b/4_processing_features/data/nf1_sc_deepprofiler_cyto.csv.gz
diff --git a/4_processing_features/data/nf1_sc_deepprofiler_nuc.csv.gz b/4_processing_features/data/nf1_sc_deepprofiler_nuc.csv.gz
diff --git a/4_processing_features/data/nf1_sc_norm_deepprofiler_cyto.csv.gz b/4_processing_features/data/nf1_sc_norm_deepprofiler_cyto.csv.gz
diff --git a/4_processing_features/data/nf1_sc_norm_deepprofiler_nuc.csv.gz b/4_processing_features/data/nf1_sc_norm_deepprofiler_nuc.csv.gz
diff --git a/4_processing_features/data/nf1_sc_norm_fs_deepprofiler_cyto.csv.gz b/4_processing_features/data/nf1_sc_norm_fs_deepprofiler_cyto.csv.gz
diff --git a/4_processing_features/data/nf1_sc_norm_fs_deepprofiler_nuc.csv.gz b/4_processing_features/data/nf1_sc_norm_fs_deepprofiler_nuc.csv.gz
diff --git a/...atures/extract_single_cell_features.ipynb → ...ing_features/extract_sc_features_cp.ipynb b/...atures/extract_single_cell_features.ipynb → ...ing_features/extract_sc_features_cp.ipynb
diff --git a/..._features/extract_single_cell_features.py → ...essing_features/extract_sc_features_cp.py b/..._features/extract_single_cell_features.py → ...essing_features/extract_sc_features_cp.py