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The Top 23 Single Cell Rna Seq Open Source Projects

Open source projects categorized as Single Cell Rna Seq
Categories > Single Cell Rna Seq
Seurat ⭐ 2,025
R toolkit for single cell genomics
dependent packages 2total releases 16most recent commit 3 months ago
Scvi Tools ⭐ 1,120
Deep probabilistic analysis of single-cell and spatial omics data
dependent packages 40total releases 71most recent commit 6 days agopypi scvi-tools} Downloads
Salmon ⭐ 661
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
most recent commit 8 months ago
Nichenetr ⭐ 416
NicheNet: predict active ligand-target links between interacting cells
most recent commit 3 months ago
Squidpy ⭐ 362
Spatial Single Cell Analysis in Python
dependent packages 33total releases 11most recent commit 3 months agopypi squidpy} Downloads
Scrna Tools ⭐ 295
Table of software for the analysis of single-cell RNA-seq data.
most recent commit 15 days ago
Dance ⭐ 284
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
total releases 4most recent commit 3 months ago
Cellrank ⭐ 279
CellRank: dynamics from multi-view single-cell data
dependent packages 4total releases 32most recent commit 4 months agopypi cellrank} Downloads
Scp ⭐ 253
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
most recent commit 4 months ago
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
Conos ⭐ 187
R package for the joint analysis of multiple single-cell RNA-seq datasets
dependent packages 1total releases 11most recent commit 2 months ago
Diffxpy ⭐ 157
Differential expression analysis for single-cell RNA-seq data.
most recent commit a year ago
Music ⭐ 156
Multi-subject Single Cell Deconvolution
most recent commit 2 years ago
Dittoseq ⭐ 153
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
most recent commit 5 months ago
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 3 months ago
Kb_python ⭐ 132
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
dependent packages 1total releases 19most recent commit 3 months agopypi kb-python} Downloads
Tidyseurat ⭐ 131
Seurat meets tidyverse. The best of both worlds.
total releases 14most recent commit 3 months ago
Numbat ⭐ 122
Haplotype-aware CNV analysis from single-cell RNA-seq
total releases 7most recent commit 6 months ago
Scpubr ⭐ 117
Generate high quality, publication ready visualizations for single cell transcriptomics data.
total releases 11most recent commit 3 months 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
Sc3 ⭐ 115
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
most recent commit 3 years ago
Sccoda ⭐ 112
A Bayesian model for compositional single-cell data analysis
dependent packages 1total releases 11most recent commit a year agopypi scCODA} Downloads
Seurat Disk ⭐ 111
Interfaces for HDF5-based Single Cell File Formats
total releases 1most recent commit 6 months ago
The 10 Most Depended On Single Cell Rna Seq Open Source Projects
Scvi Tools ⭐ 1,120
Deep probabilistic analysis of single-cell and spatial omics data
dependent packages 40total releases 71latest release December 07, 2023most recent commit 6 days agopypi scvi-tools} Downloads
Squidpy ⭐ 362
Spatial Single Cell Analysis in Python
dependent packages 33total releases 11latest release October 09, 2023most recent commit 3 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 4 months agopypi cellrank} 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
Seurat ⭐ 2,025
R toolkit for single cell genomics
dependent packages 2total releases 16latest release November 13, 2022most recent commit 3 months ago
Kb_python ⭐ 132
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
dependent packages 1total releases 19latest release November 22, 2023most recent commit 3 months agopypi kb-python} Downloads
Sccoda ⭐ 112
A Bayesian model for compositional single-cell data analysis
dependent packages 1total releases 11latest release June 29, 2022most recent commit a year agopypi scCODA} Downloads
Toolchest Client Python ⭐ 13
Toolchest Python client
dependent packages 1total releases 84latest release January 26, 2023most recent commit a year agopypi toolchest-client} Downloads
The 10 Latest Releases In Single Cell Rna Seq Open Source Projects
Scvi Tools ⭐ 1,120
Deep probabilistic analysis of single-cell and spatial omics data
dependent packages 40total releases 71latest release December 07, 2023most recent commit 6 days agopypi scvi-tools} 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
Tidyseurat ⭐ 131
Seurat meets tidyverse. The best of both worlds.
total releases 14latest release November 28, 2023most recent commit 3 months ago
Cellrank ⭐ 279
CellRank: dynamics from multi-view single-cell data
dependent packages 4total releases 32latest release November 27, 2023most recent commit 4 months agopypi cellrank} Downloads
Kb_python ⭐ 132
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
dependent packages 1total releases 19latest release November 22, 2023most recent commit 3 months agopypi kb-python} Downloads
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
Scpubr ⭐ 117
Generate high quality, publication ready visualizations for single cell transcriptomics data.
total releases 11latest release October 11, 2023most recent commit 3 months ago
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