/all_notebooks

Here you can find various (Jupyter) notebooks and bioinformatics scripts (mostly Linux shell) organized in folders depending on the topic or source

Primary LanguageJupyter Notebook

Notebooks

Here you can find various notebooks and bioinformatics scripts organized in folders depending on the topic or source. Feel free to fork or copy anything you find useful. Kaggle notebooks can also be found here, Kaggle notebooks are public under Apache 2.0 License.

Bioinformatics scripts

  1. run_broccoli.sh : runs Broccoli (orthology assignment) from a single script, requires conda.
  2. run_rnaseq_nfcore.sh : runs nf-core/rnaseq with STAR/RSEM, mouse samples (example, reference genome GRCm39).

Google Colab notebooks

  1. shap_deepexplainer_mnist_reproducibility.ipynb : reproduces DeepExplainer function applied to MNIST dataset from SHAP (SHapley Additive exPlanations) a library for Machine Learning Explainability.

Kaggle notebooks

All notebooks in this folder can be found in Kaggle. There might be one or more notebooks related to one of the following topics:

  1. 'hpa-challenge-2021': Human Protein Atlas - Single Cell Classification.
  2. 'g2net-gravitational-wave-detection-2021' : G2Net Gravitational Wave Detection.
  3. 'seti-breakthrough-listen': SETI Breakthrough Listen - E.T. Signal Search.
  4. 'leishmaniasis-reported-cases-worldwide-2005-2020': Example notebook, dataset: Neglected tropical diseases: Leishmaniasis. Reported cases by country 2005-2020.
  5. 'sartorius-competition': Sartorius - Cell Instance Segmentation, 2021.