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davisidarta/README.md

Stars

Hi! I'm David

I'm a postdoc at Ana Domingos' lab at the University of Oxford. I aim to provide a molecular, neuroanatomical, and functional characterization of the sympathetic nervous system.

My repos are a collection of tools I developed to understand and interpret high-dimensional data, and of specific projects using these tools for analyzing single-cell data. The highlight is TopoMetry, a toolkit for geometric exploration of high-dimensional data with specialized functionalities and workflows tailored for single-cell data. TopoMetry shows why using PCA or default workflows for single-cell analysis isn't a reliable approach if you want to learn from the data. The manuscript is available at eLife

I'm always open to interesting conversations. Feel free to reach me by email.

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  1. topometry topometry Public

    Systematically learn and evaluate the latent geometry of high-dimensional data, with a focus on scRNAseq analysis

    Python 105 5

  2. fastlapmap fastlapmap Public

    Fast Laplacian Eigenmaps: lightweight multicore LE for non-linear dimensional reduction with minimal memory usage. Outperforms sklearn's implementation and escalates linearly beyond 10e6 samples.

    Python 23 1

  3. humanlung humanlung Public

    Code for the human lung integrated cell atlas generation as in Sidarta-Oliveira et al.

    R 6 2

  4. dbMAP dbMAP Public

    Deprecated in favour of TopoMetry: https://github.com/davisidarta/topometry

    Python 48 4

  5. OCRC/TreinamentoSingleCell OCRC/TreinamentoSingleCell Public

    Treinamento em bioinformática de single-cell em português!

    Jupyter Notebook 2