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The Top 23 Single Cell Open Source Projects

Open source projects categorized as 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
Salmon ⭐ 661
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
most recent commit 8 months ago
Scgpt ⭐ 588
total releases 10most recent commit 3 months ago
Single Cell Best Practices ⭐ 544
https://www.sc-best-practices.org
most recent commit 4 months ago
Awesome Omics ⭐ 536
A collection of awesome things regarding all omics.
most recent commit 3 months ago
Scrna Seq_notes ⭐ 478
A list of scRNA-seq analysis tools
most recent commit 4 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
Single Cell Pseudotime ⭐ 367
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
most recent commit 3 months ago
Liger ⭐ 360
R package for integrating and analyzing multiple single-cell datasets
total releases 1most recent commit 13 days ago
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
Scrna Tools ⭐ 295
Table of software for the analysis of single-cell RNA-seq data.
most recent commit 9 days ago
Glue ⭐ 294
Graph-linked unified embedding for single-cell multi-omics data integration
most recent commit 5 months ago
Scarches ⭐ 294
Reference mapping for single-cell genomics
dependent packages 2total releases 28most recent commit 3 months agopypi scArches} Downloads
Mixcr ⭐ 291
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
most recent commit 3 months ago
Signac ⭐ 288
R toolkit for the analysis of single-cell chromatin data
dependent packages 1total releases 17most recent commit 14 days ago
Octopus ⭐ 285
Bayesian haplotype-based mutation calling
most recent commit 8 months ago
Dance ⭐ 284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
total releases 4most recent commit 3 months ago
Immunarch ⭐ 256
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
most recent commit 8 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 3 months ago
Zumis ⭐ 232
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
most recent commit a year ago
Isee ⭐ 217
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
most recent commit 14 days 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
The 10 Most Depended On Single Cell Open Source Projects
Vitessce ⭐ 124
Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
dependent packages 26total releases 18latest release November 30, 2023most recent commit 3 months agonpm @vitessce/utils} Downloads
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
Pagoda2 ⭐ 186
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
dependent packages 3total releases 9latest release December 12, 2021most recent commit 2 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
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} Downloads
Omicverse ⭐ 159
A python library for multi omics included bulk and single cell RNA-seq analysis.
dependent packages 2total releases 32latest release October 05, 2022most recent commit 3 months agopypi Pyomic} Downloads
Scarches ⭐ 294
Reference mapping for single-cell genomics
dependent packages 2total releases 28latest release December 08, 2023most recent commit 3 months agopypi scArches} Downloads
The 10 Latest Releases In Single Cell Open Source Projects
Scarches ⭐ 294
Reference mapping for single-cell genomics
dependent packages 2total releases 28latest release December 08, 2023most recent commit 3 months agopypi scArches} Downloads
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
Vitessce ⭐ 124
Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
dependent packages 26total releases 18latest release November 30, 2023most recent commit 3 months agonpm @vitessce/utils} Downloads
Tidyseurat ⭐ 131
Seurat meets tidyverse. The best of both worlds.
total releases 14latest release November 28, 2023most recent commit 3 months ago
Via ⭐ 60
trajectory inference
total releases 105latest release November 22, 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
Scgpt ⭐ 588
total releases 10latest release November 08, 2023most recent commit 3 months ago
Signac ⭐ 288
R toolkit for the analysis of single-cell chromatin data
dependent packages 1total releases 17latest release November 08, 2023most recent commit 14 days ago
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