ADD v0.4.0 docs

jmschrei · Oct 10, 2024 · 8888364 · 8888364
1 parent fa83130
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Showing 5 changed files with 20 additions and 3 deletions.
diff --git a/docs/api/ablate.rst b/docs/api/ablate.rst
@@ -2,4 +2,4 @@ ablate
 ======
 
 .. automodule:: tangermeme.ablate
-	:members: ablate
+	:members: ablate, ablate_annotations
diff --git a/docs/api/annotate.rst b/docs/api/annotate.rst
@@ -0,0 +1,5 @@
+annotate
+========
+
+.. automodule:: tangermeme.annotate
+	:members: annotate_seqlets, count_annotations, pairwise_annotations, pairwise_annotations_spacing
diff --git a/docs/api/marginalize.rst b/docs/api/marginalize.rst
@@ -2,4 +2,4 @@ marginalize
 ===========
 
 .. automodule:: tangermeme.marginalize
-	:members: marginalize
+	:members: marginalize, marginalize_annotations
diff --git a/docs/api/seqlets.rst b/docs/api/seqlets.rst
@@ -0,0 +1,5 @@
+seqlets
+=======
+
+.. automodule:: tangermeme.seqlets
+	:members: recursive_seqlets, tfmodisco_seqlets
diff --git a/docs/index.rst b/docs/index.rst
@@ -52,6 +52,8 @@ Contributions are eagerly accepted! If you would like to contribute a feature th
    tutorials/Tutorial_A1_Ersatz_Sequence_Manipulation.ipynb
    tutorials/Tutorial_A2_Predictions.ipynb
    tutorials/Tutorial_A3_Deep_LIFT_SHAP.ipynb
+   tutorials/Tutorial_A4_Seqlets.ipynb
+   tutorials/Tutorial_A5_Annotations.ipynb
    tutorials/Tutorial_B1_Marginalization.ipynb
    tutorials/Tutorial_B2_Ablation.ipynb
    tutorials/Tutorial_B3_Spacing.ipynb
@@ -63,20 +65,23 @@ Contributions are eagerly accepted! If you would like to contribute a feature th
    tutorials/Tutorial_C1_IO_and_Data_Loading.ipynb
    tutorials/Tutorial_C2_Plotting.ipynb
    tutorials/Tutorial_D1_FIMO.ipynb
+   tutorials/Tutorial_D2_TOMTOM.ipynb
 
 .. toctree::
    :maxdepth: 1
    :hidden:
    :caption: Vignettes
 
    vignettes/Attribution_Trickiness_and_DeepLiftShap_Implementations.ipynb
+   vignettes/Inspecting_What_Cis-Regulatory_Features_a_Model_Has_Learned.ipynb
 
 .. toctree::
    :maxdepth: 1
    :hidden:
    :caption: API
 
    api/ablate.rst
+   api/annotate.rst
    api/design.rst
    api/ersatz.rst
    api/io.rst
@@ -85,5 +90,7 @@ Contributions are eagerly accepted! If you would like to contribute a feature th
    api/match.rst
    api/predict.rst
    api/product.rst
+   api/seqlets.rst
    api/space.rst
-   api/variant_effect.rst
+   api/variant_effect.rst
+