Repositories list

• gh-dashboard

  Public
  A dashboard of everything in the theislab GitHub repository

  HTML

  •0•3•0•0•Updated Nov 24, 2024Nov 24, 2024

• ehrapy

  Public
  Electronic Health Record Analysis with Python.

  ehrelectronic-health-recordscverse+ 1electronic-medical-record

  Python

  •

  Apache License 2.0

  •19•235•45•4•Updated Nov 24, 2024Nov 24, 2024

• spapros

  Public
  Python package for Probe set selection for targeted spatial transcriptomics.

  Python

  •

  MIT License

  •7•28•2•9•Updated Nov 23, 2024Nov 23, 2024

• spapros-pipeline

  Public
  Nextflow

  •0•7•0•0•Updated Nov 23, 2024Nov 23, 2024

• ehrdata

  Public
  A datastructure for EHR data

  Python

  •

  Apache License 2.0

  •1•5•16•3•Updated Nov 22, 2024Nov 22, 2024

• scib

  Public
  Benchmarking analysis of data integration tools

  Python

  •

  MIT License

  •63•310•34•8•Updated Nov 22, 2024Nov 22, 2024

• cross_system_integration

  Public
  Jupyter Notebook

  •2•10•11•0•Updated Nov 21, 2024Nov 21, 2024

• zellkonverter

  Public
  Conversion between scRNA-seq objects

  rconversionscrna-seq+ 1bioconductor

  R

  •

  Other

  •28•151•11•1•Updated Nov 21, 2024Nov 21, 2024

• DRVI

  Public
  Unsupervised Deep Disentangled Representation of Single-Cell Omics

  pythonbioinformaticsintegration+ 4transcriptomicssingle-celldisentanglementanndata

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•12•0•1•Updated Nov 21, 2024Nov 21, 2024

• neural_organoid_atlas

  Public
  Reproducibility repository for the Human Neural Organoid Atlas publication

  Jupyter Notebook

  •3•21•2•1•Updated Nov 20, 2024Nov 20, 2024

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  single-celloptimal-transport

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •9•116•39•6•Updated Nov 20, 2024Nov 20, 2024

• CFGen

  Public
  Python

  •

  MIT License

  •4•6•1•0•Updated Nov 19, 2024Nov 19, 2024

• anndata2ri

  Public
  Convert between AnnData and SingleCellExperiment

  jupyterbioconductorsingle-cell+ 2rpy2scanpy

  Python

  •

  GNU General Public License v3.0

  •16•129•13•0•Updated Nov 18, 2024Nov 18, 2024

• scanpydoc

  Public
  Collection of Sphinx extensions similar to (but more flexible than) numpydoc

  Python

  •

  GNU General Public License v3.0

  •6•12•3•0•Updated Nov 18, 2024Nov 18, 2024

• multigrate

  Public
  Multigrate: multiomic data integration for single-cell genomics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•16•5•2•Updated Nov 18, 2024Nov 18, 2024

• destiny

  Public
  R package for single cell and other data analysis using diffusion maps

  rdimensionality-reductiondiffusion-maps

  R

  •

  GNU General Public License v3.0

  •11•77•31•0•Updated Nov 18, 2024Nov 18, 2024

• multimil

  Public
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•19•6•0•Updated Nov 16, 2024Nov 16, 2024

• multigrate_reproducibility

  Public
  Reproducing results from Multigrate paper

  Jupyter Notebook

  •0•3•0•0•Updated Nov 14, 2024Nov 14, 2024

• ehrapy-tutorials

  Public
  Tutorials for ehrapy

  Jupyter Notebook

  •

  Apache License 2.0

  •1•7•0•1•Updated Nov 13, 2024Nov 13, 2024

• pdac_analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• DRVI_reproducibility

  Public
  Reproducibility repository of DRVI

  Jupyter Notebook

  •0•1•0•0•Updated Nov 12, 2024Nov 12, 2024

• moscot_notebooks

  Public
  Analysis notebooks using the moscot package

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •3•7•2•4•Updated Nov 10, 2024Nov 10, 2024

• IMPA

  Public
  Jupyter Notebook

  •0•9•1•0•Updated Nov 9, 2024Nov 9, 2024

• spatialdata-db

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•25•0•Updated Nov 8, 2024Nov 8, 2024

• GoBI_single_cell

  Public
  Single-cell worksheet and notes for the GoBI bachelor course 2021

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• single-cell-best-practices

  Public
  https://www.sc-best-practices.org

  tutorialrna-seqbook+ 1single-cell

  Jupyter Notebook

  •

  Other

  •189•784•70•3•Updated Nov 4, 2024Nov 4, 2024

• archmap_data

  Public
  Python

  •0•1•1•1•Updated Nov 3, 2024Nov 3, 2024

• task-dge-perturbation-prediction-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •1•4•0•0•Updated Oct 30, 2024Oct 30, 2024

• pertpy-reproducibility

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •1•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• archmap

  Public
  JavaScript

  •

  MIT License

  •0•4•3•0•Updated Oct 29, 2024Oct 29, 2024