Theis Lab

Repositories

• squidpy

  Spatial Single Cell Analysis in Python
  Python BSD-3-Clause 10 58 28 (1 issue needs help) 5 Updated May 12, 2021

• scvelo

  RNA Velocity generalized through dynamical modeling
  Python BSD-3-Clause 53 195 97 2 Updated May 12, 2021

• scanpy

  Single-Cell Analysis in Python. Scales to >1M cells.

  data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata
  Python BSD-3-Clause 331 886 339 (7 issues need help) 49 Updated May 12, 2021

• scArches-reproducibility

  Reproducing result from the paper
  Jupyter Notebook 0 4 0 0 Updated May 12, 2021

• sfaira-portal

  Code for the Sfaira Portal website

  website rna-seq database single-cell tailwindcss vue3 vite
  Vue MIT 0 0 0 0 Updated May 12, 2021

• sfaira

  data and model repository for single-cell data
  Python BSD-3-Clause 1 63 73 5 Updated May 12, 2021

• spapros

  Fully automated spatial transcriptomics probe selection.
  Python MIT 0 1 1 4 Updated May 12, 2021

• anndata

  Annotated data.

  data-science machine-learning bioinformatics transcriptomics scanpy
  Python BSD-3-Clause 79 178 112 (1 issue needs help) 30 Updated May 12, 2021

• zellkonverter

  Conversion between scRNA-seq objects

  r conversion bioconductor scrna-seq
  R 6 37 8 2 Updated May 11, 2021

• cellrank

  CellRank for directed single-cell fate mapping

  data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning
  Python BSD-3-Clause 6 106 9 1 Updated May 9, 2021

• disent

  Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data
  Jupyter Notebook BSD-3-Clause 0 1 0 0 Updated May 8, 2021

• scib-reproducibility

  Additional code and analysis from the single-cell integration benchmarking project

  website benchmarking rna-seq integration scrna-seq results single-cell
  Jupyter Notebook MIT 1 2 0 2 Updated May 7, 2021

• scib-pipeline

  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  Python MIT 1 2 1 0 Updated May 7, 2021

• scCODA

  A statistical test for compositional changes in scRNA

  tensorflow
  Jupyter Notebook BSD-3-Clause 4 45 1 0 Updated May 7, 2021

• scib

  Benchmarking analysis of data integration tools
  Jupyter Notebook MIT 12 86 8 8 Updated May 7, 2021

• squidpy_notebooks

  Tutorials for Squidpy
  Python MIT 1 3 3 0 Updated May 6, 2021

• scanpydoc

  Collection of Sphinx extensions similar to (but more flexible than) numpydoc
  Python GPL-3.0 3 7 2 2 Updated May 5, 2021

• squidpy_reproducibility
  Jupyter Notebook BSD-3-Clause 0 1 0 3 Updated May 1, 2021

• scgen

  Single cell perturbation prediction

  bioinformatics deep-learning generative-model transcriptomics single-cell
  Python GPL-3.0 27 128 14 0 Updated Apr 30, 2021

• scarches

  Query to reference mapping for single-cell genomics

  deep-learning data-integration single-cell rna-seq-analysis batch-correction
  Jupyter Notebook 10 73 6 2 Updated Apr 29, 2021

• gut_lineage
  Jupyter Notebook 1 2 0 0 Updated Apr 28, 2021

• intercode
  Jupyter Notebook BSD-3-Clause 1 2 0 1 Updated Apr 13, 2021

• cellrank_notebooks

  Tutorials and figures for CellRank

  tutorials figures cellrank
  Jupyter Notebook BSD-3-Clause 1 2 0 0 Updated Apr 9, 2021

• LODE

  repository for all LODE projects
  Jupyter Notebook 0 2 0 2 Updated Apr 6, 2021

• DeepRT
  Jupyter Notebook MIT 5 11 0 3 Updated Mar 25, 2021

• scanpy-tutorials

  Scanpy Tutorials.
  Jupyter Notebook 38 48 10 2 Updated Mar 25, 2021

• dca

  Deep count autoencoder for denoising scRNA-seq data
  Python Apache-2.0 53 171 13 0 Updated Mar 21, 2021

• InterpretableAutoencoders
  Jupyter Notebook 1 4 0 0 Updated Mar 17, 2021

• sfaira_extension
  Python BSD-3-Clause 0 0 1 0 Updated Mar 11, 2021

• diffxpy

  Differential expression analysis for single-cell RNA-seq data.

  bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq
  Python BSD-3-Clause 24 91 81 7 Updated Mar 9, 2021