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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"single-cell-best-practices
https://www.sc-best-practices.orgscvelo
RNA Velocity generalized through dynamical modelingscarches
Reference mapping for single-cell genomicscellrank
CellRank: dynamics from multi-view single-cell datascib
Benchmarking analysis of data integration toolsscgen
Single cell perturbation predictiondca
Deep count autoencoder for denoising scRNA-seq datadiffxpy
Differential expression analysis for single-cell RNA-seq data.paga
Mapping out the coarse-grained connectivity structures of complex manifolds.kBET
An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.scCODA
A Bayesian model for compositional single-cell data analysissfaira
data and model repository for single-cell datasc-pert
Models and datasets for perturbational single-cell omicsanndata2ri
Convert between AnnData and SingleCellExperimentehrapy
Electronic Health Record Analysis with Python.ncem
Learning cell communication from spatial graphs of cellsmoscot
Multi-omic single-cell optimal transport toolschemCPA
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.zellkonverter
Conversion between scRNA-seq objectspertpy
Perturbation Analysis in the scverse ecosystem.cpa
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.destiny
R package for single cell and other data analysis using diffusion mapsscib-pipeline
Snakemake pipeline that works with the scIB package to benchmark data integration methods.trVAE
Conditional out-of-distribution predictionscib-reproducibility
Additional code and analysis from the single-cell integration benchmarking projectAutoGeneS
spatial_scog_workshop_2022
Tutorials for the SCOG Virtual Workshop βSpatial transcriptomics data analysis in Pythonβ - May 23-24, 2022pseudodynamics
Dynamic models for single-cell RNA-seq time series.tcellmatch
scArches-reproducibility
Reproducing result from the paperscTab
deepflow
This code contains the neural network implementation from the nature communication manuscript NCOMMS-16-25447A.batchglm
Fit generalized linear models in python.graph_abstraction
Generate cellular maps of differentiation manifolds with complex topologies.DeepRT
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"hadge
Comprehensive pipeline for donor demultiplexing in single cellscvelo_notebooks
spapros
Python package for Probe set selection for targeted spatial transcriptomics.interactive_plotting
nicheformer
Repository for Nicheformer: a foundation model for single-cell and spatial omicsscgen-reproducibility
geome
graphcompass
GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systemsmulticpa
campa
Conditional Autoencoders for Multiplexed Pixel Analysiscellrank_reproducibility
CellRank's reproducibility repository.scanpy-in-R
A guide to using the Python scRNA-seq analysis package Scanpy from Rscanpydoc
Collection of Sphinx extensions similar to (but more flexible than) numpydocscPoli_reproduce
Reproducibility notebooks for scPoliDeepCollisionalCrossSection
MetaMap
The code and analyses accompanying the manuscript βMetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq dataβ.scAnalysisTutorial
multigrate
Multigrate: multiomic data integration for single-cell genomicsGWAS-scRNAseq-Integration
A Shiny tool to define the cell-type of action by integrating single cell expression data with GWASsuperexacttestpy
Python implementation of the SuperExactTest packageenrichment_analysis_celltype
Cell type enrichment analysis using gene signatures and cluster markersncem_tutorials
moslin
Code, data and analysis for moslin.diffxpy_tutorials
Tutorials for diffxpy.cross_system_integration
trvaep
expiMap_reproducibility
greatpy
GREAT algorithm in PythonPathReg
Sparsity-enforcing regularizerIMPA
ncem_benchmarks
squidpy_reproducibility
sc-best-practices-ce
The best-practices workflow for single-cell RNA-seq analysis as determined by the community.tissue_tensorflow
scachepy
Caching extension for Scanpycpa-reproducibility
Notebooks for CPA figuresscCODA_reproducibility
2020_Mayr
This repo contains the analysis code describing the findings of Mayr_et_algastrulation_analysis
2019_Strunz
Reproducibility repo accompanying Strunz et al. "Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis". Nat Commun. 2020.trVAE_reproducibility
cellrank_notebooks
Tutorials and examples for CellRank.moscot_notebooks
Analysis notebooks using the moscot packageintercode
spapros-pipeline
ehrapy-tutorials
Tutorials for ehrapysfaira_tutorials
flowVI
flowVI: Flow Cytometry Variational Inference2018_Angelidis
Reproducibility repo accompanying Angelidis et al. "An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics"InterpretableAutoencoders
theislab.github.io
theislab repository overviewdisent
Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing dataehrapy-datasets
A collection of scripts to generate AnnData objects of EHR datasets for ehrapyneural_organoid_atlas
Reproducibility repository for the Human Neural Organoid Atlas publicationscatac_poisson_reproducibility
scanpy-demo-czbiohub
single-cell scanpy teachingkbranches
Finding branching events and tips in single cell differentiation trajectoriesjump-cpg0016-segmentation
Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortiumcellrank_reproducibility_preprint
Code to reproduce results from the CellRank preprintinVAE
Invariant Representation learningextended-single-cell-best-practices-container
Hosting the container for the extended single-cell best-practices bookperturbation-metrics
LODE
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