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The Top 23 Single Cell Transcriptomics Open Source Projects

Open source projects categorized as Single Cell Transcriptomics
Categories > Single Cell
Categories > Transcriptomics
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
Isee ⭐ 217
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
most recent commit 20 days ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9most recent commit 7 months agopypi scgen} Downloads
Pagoda2 ⭐ 191
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
dependent packages 3total releases 9most recent commit 2 months ago
Sccatch ⭐ 171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 5most recent commit a year ago
Scde ⭐ 163
R package for analyzing single-cell RNA-seq data
most recent commit a year ago
Alevin Fry ⭐ 115
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
dependent packages 2total releases 10most recent commit 10 months agocargo libradicl} Downloads
Decoupler Py ⭐ 112
Python package to perform enrichment analysis from omics data.
dependent packages 3total releases 10most recent commit 3 months agopypi decoupler} Downloads
Scdeepsort ⭐ 93
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
most recent commit 10 months ago
Pando ⭐ 88
Multiome GRN inference.
most recent commit 3 months ago
Singlecellhaystack ⭐ 68
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
most recent commit 3 months ago
Mudan ⭐ 66
Multi-sample Unified Discriminant ANalysis
most recent commit a year ago
Cirrocumulus ⭐ 55
Bring your single-cell data to life
total releases 147most recent commit 5 months ago
Ewce ⭐ 46
Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
most recent commit 5 months ago
Celltalker ⭐ 41
Inference of cell-cell communication from single-cell RNAseq data
most recent commit 10 months ago
Spatialtranscriptomics ⭐ 34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
most recent commit 3 months ago
Scpa ⭐ 33
R package for pathway analysis in scRNA-seq data
most recent commit 6 months ago
Asap ⭐ 24
ASAP : Automated Single-cell Analysis Pipeline
most recent commit 4 months ago
Omicssuite.github.io ⭐ 15
OmicsSuite website for releasing new version.
most recent commit 3 months ago
Scasa ⭐ 12
SCASA: Single cell transcript quantification tool
most recent commit 5 months ago
Topicvelo ⭐ 11
TopicVelo: Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems
most recent commit 4 months ago
Hummus ⭐ 9
Molecular interactions inference from single-cell multi-omics data
most recent commit 4 months ago
Iasva ⭐ 8
Iteratively Adjusted Surrogate Variable Analysis
most recent commit 3 years ago
The 5 Most Depended On Single Cell Transcriptomics Open Source Projects
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
Pagoda2 ⭐ 191
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
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} Downloads
The 8 Latest Releases In Single Cell Transcriptomics Open Source Projects
Cirrocumulus ⭐ 55
Bring your single-cell data to life
total releases 147latest release September 29, 2023most recent commit 5 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
Sccatch ⭐ 171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 5latest release April 23, 2023most recent commit a year ago
Scgen ⭐ 215
Single cell perturbation prediction
dependent packages 2total releases 9latest release April 25, 2022most recent commit 7 months agopypi scgen} Downloads
Pagoda2 ⭐ 191
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
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