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The Top 23 Single Cell Genomics Open Source Projects

Open source projects categorized as Single Cell Genomics
Categories > Single Cell Genomics
Seurat ⭐ 2,025
R toolkit for single cell genomics
dependent packages 2total releases 16most recent commit 5 months ago
Scvi Tools ⭐ 1,140
Deep probabilistic analysis of single-cell and spatial omics data
dependent packages 40total releases 71most recent commit 17 days agopypi scvi-tools} Downloads
Squidpy ⭐ 362
Spatial Single Cell Analysis in Python
dependent packages 33total releases 11most recent commit 5 months agopypi squidpy} Downloads
Scarches ⭐ 294
Reference mapping for single-cell genomics
dependent packages 2total releases 28most recent commit 5 months agopypi scArches} Downloads
Cellrank ⭐ 279
CellRank: dynamics from multi-view single-cell data
dependent packages 4total releases 32most recent commit 5 months agopypi cellrank} Downloads
Seurat Wrappers ⭐ 268
Community-provided extensions to Seurat
most recent commit 4 months ago
Scp ⭐ 253
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
most recent commit 5 months ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 8 months agopypi scgen} Downloads
Palantir ⭐ 184
Single cell trajectory detection
dependent packages 2total releases 10most recent commit 5 months agopypi palantir} Downloads
Sccustomize ⭐ 142
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
total releases 5most recent commit 5 months ago
Snapatac2 ⭐ 133
Single-cell epigenomics analysis tools
most recent commit 5 months ago
Scpubr ⭐ 117
Generate high quality, publication ready visualizations for single cell transcriptomics data.
total releases 11most recent commit 4 months ago
Seurat Disk ⭐ 111
Interfaces for HDF5-based Single Cell File Formats
total releases 1most recent commit 7 months ago
Seurat Data ⭐ 101
Dataset distribution for Seurat
most recent commit 7 months ago
Swne ⭐ 100
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
most recent commit 10 months ago
Scarf ⭐ 83
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
dependent packages 1total releases 43most recent commit 4 months agopypi scarf} Downloads
Azimuth ⭐ 79
A Shiny web app for mapping datasets using Seurat v4
most recent commit 7 months ago
Scnym ⭐ 71
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
total releases 5most recent commit 6 months ago
Single_cell_portal_core ⭐ 60
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
most recent commit 4 months ago
Cpa ⭐ 55
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.
total releases 32most recent commit 7 months ago
Scalex ⭐ 55
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
total releases 21most recent commit 8 months ago
Celldancer ⭐ 46
Predict RNA velocity through deep learning
most recent commit 6 months ago
Ginkgo ⭐ 44
Cloud-based single-cell copy-number variation analysis tool
most recent commit a year ago
The 8 Most Depended On Single Cell Genomics Open Source Projects
Scvi Tools ⭐ 1,140
Deep probabilistic analysis of single-cell and spatial omics data
dependent packages 40total releases 71latest release December 07, 2023most recent commit 17 days agopypi scvi-tools} Downloads
Squidpy ⭐ 362
Spatial Single Cell Analysis in Python
dependent packages 33total releases 11latest release October 09, 2023most recent commit 5 months agopypi squidpy} Downloads
Cellrank ⭐ 279
CellRank: dynamics from multi-view single-cell data
dependent packages 4total releases 32latest release November 27, 2023most recent commit 5 months agopypi cellrank} Downloads
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 8 months agopypi scgen} Downloads
Palantir ⭐ 184
Single cell trajectory detection
dependent packages 2total releases 10latest release November 29, 2023most recent commit 5 months agopypi palantir} Downloads
Seurat ⭐ 2,025
R toolkit for single cell genomics
dependent packages 2total releases 16latest release November 13, 2022most recent commit 5 months ago
Scarches ⭐ 294
Reference mapping for single-cell genomics
dependent packages 2total releases 28latest release December 08, 2023most recent commit 5 months agopypi scArches} Downloads
The 10 Latest Releases In Single Cell Genomics Open Source Projects
Scarches ⭐ 294
Reference mapping for single-cell genomics
dependent packages 2total releases 28latest release December 08, 2023most recent commit 5 months agopypi scArches} Downloads
Scvi Tools ⭐ 1,140
Deep probabilistic analysis of single-cell and spatial omics data
dependent packages 40total releases 71latest release December 07, 2023most recent commit 17 days agopypi scvi-tools} Downloads
Palantir ⭐ 184
Single cell trajectory detection
dependent packages 2total releases 10latest release November 29, 2023most recent commit 5 months agopypi palantir} Downloads
Cellrank ⭐ 279
CellRank: dynamics from multi-view single-cell data
dependent packages 4total releases 32latest release November 27, 2023most recent commit 5 months agopypi cellrank} Downloads
Scpubr ⭐ 117
Generate high quality, publication ready visualizations for single cell transcriptomics data.
total releases 11latest release October 11, 2023most recent commit 4 months ago
Squidpy ⭐ 362
Spatial Single Cell Analysis in Python
dependent packages 33total releases 11latest release October 09, 2023most recent commit 5 months agopypi squidpy} Downloads
Pyrovelocity ⭐ 31
𝒫robabilistic modeling of RNA velocity ⬱
total releases 3latest release September 06, 2023most recent commit 5 months ago
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