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The Top 14 Single Cell Gene Expression Open Source Projects

Open source projects categorized as Single Cell Gene Expression
Categories > Gene Expression
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
Isee ⭐ 217
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
most recent commit 21 days ago
Powsimr ⭐ 102
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
most recent commit 9 months ago
Basics ⭐ 81
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
most recent commit 4 months ago
Scope ⭐ 56
Fast visualization tool for large-scale and high dimensional single-cell data
most recent commit 2 years ago
Meringue ⭐ 33
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
most recent commit 2 years ago
Ouija ⭐ 29
Descriptive probabilistic marker gene approach to single-cell pseudotime inference
most recent commit 4 years ago
Scnanogps ⭐ 29
Single cell Nanopore sequencing data for Genotype and Phenotype
most recent commit 3 months ago
Clonealign ⭐ 25
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
most recent commit 3 years ago
Asap ⭐ 24
ASAP : Automated Single-cell Analysis Pipeline
most recent commit 4 months ago
Switchde ⭐ 15
Inference of switch-like differential expression along single-cell trajectories
most recent commit 7 years ago
Gear ⭐ 10
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
most recent commit 5 months ago
Resvae ⭐ 7
resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.
most recent commit a year ago
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