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2022univr-medbioinfo

Teaching material for spatial transcriptomics session, Medical Bioinformatics, UNIVR

awesome_spatial_omics

tools and notes for spatial omics

ciclo

A functional training loops library for JAX

due

Code for "On Feature Collapse and Deep Kernel Learning for Single Forward Pass Uncertainty".

eggplant

giovp.github.io

✨ Build a beautiful and simple website in literally minutes. Demo at https://beautifuljekyll.com

ifom-tutorials-2023

lamindb

Manage R&D data and analyses.

latent_factors_autoimmune

lnschema-lamin1

multiscale-spatial-image

Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.

napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

ome-zarr-py

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

ott

Optimal Transport tools implemented with the JAX framework, to get auto-diff, parallel and jit-able computations.

paste

Probabilistic Alignment of Spatial Transcriptomics Experiments

pointpats

Planar Point Pattern Analysis in PySAL

pydantic-ome-ngff

Pydantic models for OME-NGFF

random-promoter-dream-challenge-2022

scanpy-tutorials

Scanpy Tutorials.

schist

An interface for Nested Stochastic Block Model for single cell analysis

sclecture21

Project repo for sc analysis course

scvi-tools

Deep probabilistic analysis of single-cell omics data

singlecellopenproblems

Formalizing and benchmarking open problems in single-cell genomics

spatial-alignment

Alignment of spatial genomics data using deep Gaussian processes

spatial-image

A multi-dimensional spatial image data structure for scientific Python.

spatial-scripts

spatialdata

spatialdata-sandbox

squidpy-feedstock

A conda-smithy repository for squidpy.