Theis Lab

Repositories

• sfaira

  data and model repository for single-cell data
  Python BSD-3-Clause 0 46 34 2 Updated Jan 17, 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 291 814 336 (7 issues need help) 49 Updated Jan 17, 2021

• scArches-reproducibility

  Reproducing result from the paper
  Jupyter Notebook 0 4 0 0 Updated Jan 15, 2021

• cellrank_notebooks

  Tutorials and figures for CellRank

  tutorials figures cellrank
  Jupyter Notebook BSD-3-Clause 1 2 0 0 Updated Jan 15, 2021

• cellrank

  Probabilistic Fate Mapping using RNA Velocity

  data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning
  Python BSD-3-Clause 6 76 4 0 Updated Jan 15, 2021

• scarches

  architecture surgery and transfer learning for single-cell

  deep-learning single-cell rna-seq-analysis
  Jupyter Notebook 8 44 1 0 Updated Jan 14, 2021

• scanpy-tutorials

  Scanpy Tutorials.
  Jupyter Notebook 32 38 9 2 Updated Jan 14, 2021

• scib-pipeline

  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  Python MIT 0 1 0 1 Updated Jan 12, 2021

• scib

  Benchmarking analysis of data integration tools
  Jupyter Notebook MIT 9 64 11 7 Updated Jan 12, 2021

• scib-reproducibility

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

  website benchmarking rna-seq integration scrna-seq results single-cell
  R MIT 0 2 0 0 Updated Jan 12, 2021

• anndata

  Annotated data.

  data-science machine-learning bioinformatics transcriptomics scanpy
  Python BSD-3-Clause 68 153 90 (1 issue needs help) 24 Updated Jan 12, 2021

• anndata2ri

  Convert between AnnData and SingleCellExperiment

  jupyter bioconductor single-cell rpy2 scanpy
  Python 8 41 6 0 Updated Jan 10, 2021

• scCODA

  A statistical test for compositional changes in scRNA

  tensorflow
  Jupyter Notebook BSD-3-Clause 3 25 1 0 Updated Jan 8, 2021

• trVAE

  Conditional out-of-distribution prediction

  deep-learning generative-model mmd single-cell cvae
  Python MIT 4 30 1 1 Updated Jan 7, 2021

• LODE

  repository for all LODE projects
  Jupyter Notebook 0 2 0 1 Updated Jan 6, 2021

• single-cell-tutorial

  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
  Jupyter Notebook 217 541 4 2 Updated Jan 5, 2021

• sfaira_extension
  Python BSD-3-Clause 0 0 1 0 Updated Jan 4, 2021

• Covid_meta_analysis

  Analysis notebooks for the Covid-19 meta analysis that accompanies the Nature Medicine publication "Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics"
  Jupyter Notebook MIT 1 3 1 0 Updated Dec 22, 2020

• sc-pert

  Models and datasets for perturbational single-cell omics
  MIT 0 0 0 0 Updated Dec 20, 2020

• zellkonverter

  Conversion between scRNA-seq objects

  r conversion bioconductor scrna-seq
  R 5 23 7 0 Updated Dec 19, 2020

• 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 20 77 72 7 Updated Dec 18, 2020

• scarchesp
  Jupyter Notebook 0 1 7 0 Updated Dec 16, 2020

• ipsc_ipd_analysis

  The analysis scripts that were used for the analysis of iPSc iPD patient and cell line data.
  Jupyter Notebook 0 0 0 0 Updated Dec 14, 2020

• sfaira-site

  Website displaying the sfaira database
  R 0 0 0 0 Updated Dec 14, 2020

• scCODA_reproducibility
  Jupyter Notebook MIT 1 0 0 0 Updated Dec 10, 2020

• scvelo

  RNA Velocity generalized through dynamical modeling
  Python BSD-3-Clause 45 162 69 3 Updated Dec 9, 2020

• scanpy.org
  0 0 1 0 Updated Dec 9, 2020

• scvelo_notebooks
  Jupyter Notebook 5 12 1 0 Updated Dec 4, 2020

• scgen

  Single cell perturbation prediction

  bioinformatics deep-learning generative-model transcriptomics
  Python GPL-3.0 24 118 12 1 Updated Dec 1, 2020

• interaction-tools

  Information about cell-cell interaction tools and examples of how they are used
  R MIT 0 0 0 0 Updated Nov 24, 2020