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"

✭ 594

jupyter-notebook

9. scarches

Reference mapping for single-cell genomics

✭ 175

Jupyter Notebook python deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas

10. zellkonverter

Conversion between scRNA-seq objects

✭ 67

r shell conversion bioconductor scrna-seq

11. sfaira

data and model repository for single-cell data

✭ 119

python shell

12. batchglm

Fit generalized linear models in python.

✭ 22

python tensorflow differential-expression generalized-linear-models

13. diffxpy

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

✭ 137

python bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq

14. squidpy

Spatial Single Cell Analysis in Python

✭ 235

python shell data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy

15. ncem

Learning cell communication from spatial graphs of cells

✭ 77

python tensorflow glm cvae encoder-decoder-model gnn scanpy cell-cell-interaction cell-cell-communication squidpy

16. anndata2ri

Convert between AnnData and SingleCellExperiment

✭ 79

python Jupyter Notebook jupyter bioconductor single-cell rpy2 scanpy

17. trVAE

Conditional out-of-distribution prediction

✭ 47

python deep-learning generative-model mmd single-cell cvae

18. cellrank

CellRank for directed single-cell fate mapping

✭ 222

python shell data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions fuzzy-clustering-analyses rna-velocity cell-fate-determination

19. scCODA

A Bayesian model for compositional single-cell data analysis

✭ 109

Jupyter Notebook python tensorflow statistical-analysis single-cell-rna-seq compositional-changes

20. graph abstraction

Generate cellular maps of differentiation manifolds with complex topologies.

✭ 26

Jupyter Notebook r

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