From 8888364df09a0f31a579402bb4548e116e90828d Mon Sep 17 00:00:00 2001 From: Jacob Schreiber Date: Thu, 10 Oct 2024 10:01:52 +0000 Subject: [PATCH] ADD v0.4.0 docs --- docs/api/ablate.rst | 2 +- docs/api/annotate.rst | 5 +++++ docs/api/marginalize.rst | 2 +- docs/api/seqlets.rst | 5 +++++ docs/index.rst | 9 ++++++++- 5 files changed, 20 insertions(+), 3 deletions(-) create mode 100644 docs/api/annotate.rst create mode 100644 docs/api/seqlets.rst diff --git a/docs/api/ablate.rst b/docs/api/ablate.rst index 1821d16..61ccfb9 100644 --- a/docs/api/ablate.rst +++ b/docs/api/ablate.rst @@ -2,4 +2,4 @@ ablate ====== .. automodule:: tangermeme.ablate - :members: ablate \ No newline at end of file + :members: ablate, ablate_annotations \ No newline at end of file diff --git a/docs/api/annotate.rst b/docs/api/annotate.rst new file mode 100644 index 0000000..c37a3a8 --- /dev/null +++ b/docs/api/annotate.rst @@ -0,0 +1,5 @@ +annotate +======== + +.. automodule:: tangermeme.annotate + :members: annotate_seqlets, count_annotations, pairwise_annotations, pairwise_annotations_spacing \ No newline at end of file diff --git a/docs/api/marginalize.rst b/docs/api/marginalize.rst index 83a92b4..fac5e57 100644 --- a/docs/api/marginalize.rst +++ b/docs/api/marginalize.rst @@ -2,4 +2,4 @@ marginalize =========== .. automodule:: tangermeme.marginalize - :members: marginalize \ No newline at end of file + :members: marginalize, marginalize_annotations \ No newline at end of file diff --git a/docs/api/seqlets.rst b/docs/api/seqlets.rst new file mode 100644 index 0000000..f5a7389 --- /dev/null +++ b/docs/api/seqlets.rst @@ -0,0 +1,5 @@ +seqlets +======= + +.. automodule:: tangermeme.seqlets + :members: recursive_seqlets, tfmodisco_seqlets \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 5f5c320..cb0b1fd 100644 --- 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 @@ -63,6 +65,7 @@ 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 @@ -70,6 +73,7 @@ Contributions are eagerly accepted! If you would like to contribute a feature th :caption: Vignettes vignettes/Attribution_Trickiness_and_DeepLiftShap_Implementations.ipynb + vignettes/Inspecting_What_Cis-Regulatory_Features_a_Model_Has_Learned.ipynb .. toctree:: :maxdepth: 1 @@ -77,6 +81,7 @@ Contributions are eagerly accepted! If you would like to contribute a feature th :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 \ No newline at end of file + api/variant_effect.rst + \ No newline at end of file