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The Top 23 Python Single Cell Open Source Projects

Open source projects categorized as Python Single Cell
Categories > Single Cell
Awesome Single Cell ⭐ 2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
most recent commit 3 months ago
Phate ⭐ 421
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
dependent packages 14total releases 36most recent commit 10 months agopypi phate} Downloads
Pyscenic ⭐ 321
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
dependent packages 6total releases 63most recent commit 9 months agopypi pyscenic} Downloads
Glue ⭐ 294
Graph-linked unified embedding for single-cell multi-omics data integration
most recent commit 5 months ago
Dance ⭐ 284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
total releases 4most recent commit 3 months ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 7 months agopypi scgen} Downloads
Celltypist ⭐ 202
A tool for semi-automatic cell type classification
dependent packages 1total releases 24most recent commit 6 months agopypi celltypist} Downloads
Stream ⭐ 163
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
most recent commit 2 years ago
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10most recent commit 3 months agopypi decoupler} Downloads
Deepcpg ⭐ 108
Deep neural networks for predicting CpG methylation
total releases 8most recent commit 5 years ago
Anndata2ri ⭐ 104
Convert between AnnData and SingleCellExperiment
dependent packages 4total releases 11most recent commit 3 months agopypi anndata2ri} Downloads
Liana Py ⭐ 99
LIANA+: an all-in-one framework for cell-cell communication
total releases 14most recent commit 3 months ago
Infercnvpy ⭐ 97
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
dependent packages 2total releases 9most recent commit 3 months agopypi infercnvpy} Downloads
Scatac Benchmarking ⭐ 92
Benchmarking computational single cell ATAC-seq methods
most recent commit 3 years ago
Mgatk ⭐ 89
mgatk: mitochondrial genome analysis toolkit
total releases 20most recent commit 3 months ago
Sinto ⭐ 86
Tools for single-cell data processing
total releases 32most recent commit 8 months ago
Moscot ⭐ 81
Multi-omic single-cell optimal transport tools
total releases 6most recent commit 3 months ago
Cell_blast ⭐ 74
A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
total releases 8most recent commit 9 months ago
Scnym ⭐ 71
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
total releases 5most recent commit 4 months ago
Pertpy ⭐ 69
Perturbation Analysis in the scverse ecosystem.
total releases 6most recent commit 3 months ago
Topometry ⭐ 69
Systematically learn and evaluate manifolds from high-dimensional data
total releases 26most recent commit 10 months ago
Covid 19 Rna Seq Datasets ⭐ 61
A repository for sharing information on available COVID-19 RNA-Seq datasets
most recent commit 2 years ago
Scperturb ⭐ 56
scPerturb: A resource and a python/R tool for single-cell perturbation data
total releases 5most recent commit 3 months ago
The 9 Most Depended On Python Single Cell Open Source Projects
Phate ⭐ 421
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
dependent packages 14total releases 36latest release August 13, 2018most recent commit 10 months agopypi phate} Downloads
Anndata2ri ⭐ 104
Convert between AnnData and SingleCellExperiment
dependent packages 4total releases 11latest release August 24, 2023most recent commit 3 months agopypi anndata2ri} Downloads
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10latest release August 31, 2023most recent commit 3 months agopypi decoupler} Downloads
Infercnvpy ⭐ 97
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
dependent packages 2total releases 9latest release September 26, 2023most recent commit 3 months agopypi infercnvpy} Downloads
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} Downloads
Vitessce Python ⭐ 28
Python API and Jupyter widget for Vitessce
dependent packages 1total releases 15latest release December 15, 2022most recent commit 3 months agonpm vitessce-jupyter} Downloads
Pyliger ⭐ 19
Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)
dependent packages 1total releases 8latest release August 30, 2023most recent commit 8 months agopypi pyliger} Downloads
Celltypist ⭐ 202
A tool for semi-automatic cell type classification
dependent packages 1total releases 24latest release November 01, 2023most recent commit 6 months agopypi celltypist} Downloads
The 10 Latest Releases In Python Single Cell Open Source Projects
Dance ⭐ 284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
total releases 4latest release December 04, 2023most recent commit 3 months ago
Liana Py ⭐ 99
LIANA+: an all-in-one framework for cell-cell communication
total releases 14latest release November 10, 2023most recent commit 3 months ago
Pertpy ⭐ 69
Perturbation Analysis in the scverse ecosystem.
total releases 6latest release November 02, 2023most recent commit 3 months ago
Celltypist ⭐ 202
A tool for semi-automatic cell type classification
dependent packages 1total releases 24latest release November 01, 2023most recent commit 6 months agopypi celltypist} Downloads
Moscot ⭐ 81
Multi-omic single-cell optimal transport tools
total releases 6latest release October 09, 2023most recent commit 3 months ago
Infercnvpy ⭐ 97
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
dependent packages 2total releases 9latest release September 26, 2023most recent commit 3 months agopypi infercnvpy} Downloads
Scperturb ⭐ 56
scPerturb: A resource and a python/R tool for single-cell perturbation data
total releases 5latest release September 25, 2023most recent commit 3 months ago
Sinto ⭐ 86
Tools for single-cell data processing
total releases 32latest release September 07, 2023most recent commit 8 months ago
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10latest release August 31, 2023most recent commit 3 months agopypi decoupler} Downloads
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