96 Open Source Single Cell Rna Seq Software Projects

R toolkit for single cell genomics

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Table of software for the analysis of single-cell RNA-seq data.

R package for the joint analysis of multiple single-cell RNA-seq datasets

NicheNet: predict active ligand-target links between interacting cells

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

Multi-subject Single Cell Deconvolution

Differential expression analysis for single-cell RNA-seq data.

A collection of 50+ trajectory inference methods within a common interface 📥📤

A tool for unsupervised projection of single cell RNA-seq data

integrated RNA-seq Analysis Pipeline

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

Accurate and robust imputation of scRNA-seq data

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Single-Cell Clustering Assessment Framework

Clustering cells from single cell RNA seq assays

scDeepCluster for Single Cell RNA-seq data

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

An R-based interface for loom files

An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

Clone of the Bioconductor repository for the DropletUtils package.

Clone of the Bioconductor repository for the scran package.

Bayesian MCMC matrix factorization algorithm

:hibiscus: reference-free transcriptome assembly for short and long reads

Wasserstein Generative Adversarial Network for analysing scRNAseq data

Dynamic models for single-cell RNA-seq time series.

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

Single-cell exploratory data analysis for RNA-Seq

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

Metacell - Single-cell mRNA Analysis

CellRank for directed single-cell fate mapping

Stacked Denoising AutoEncoder based on TensorFlow

A R framework for pipeline benchmarking, with application to single-cell RNAseq

A Library for Denoising Single-Cell Data with Random Matrix Theory

Processing of single cell RNAseq data for the recovery of TCRs in python

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

All-in-one analysis pipeline

Deep Learning based cell composition analysis with Scaden.

Data and analysis for the Splatter paper

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Code for the empty droplet and cell detection project from the HCA Hackathon.

Content for the OSCA Book.

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Tutorial for the analysis of scRNA-seq data in R

Discrete Distributional Differential Expression

tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data

Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations

Interfaces for HDF5-based Single Cell File Formats

SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.

An analytics package for single cell data

Deep probabilistic analysis of single-cell omics data

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

Marker gene selection from scRNA-seq data

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Predict cell cycle phase in a continuum from single-cell RNA-seq data

Spatial Single Cell Analysis in Python

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Seurat meets tidyverse. The best of both worlds.

A statistical test for compositional changes in scRNA

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

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.

A Shiny web app for mapping datasets using Seurat v4

R package to visualize gene expression data based on weighted kernel density estimation

scLearn：Learning for single cell assignment

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

Single-cell Orientation Tracing

Signac

scDCC: Single Cell Deep Constrained Clustering

Manuscript for functional prediction of transcriptomic “dark matter” across species

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It provides users with a flexibility of choosing a machine learning based classifiers or let ELeFHAnt automatically use the power of robust classifiers like randomForest and SVM (Support Vector Machines) to make predictions. It has three functions 1) CelltypeAnnotation 2) LabelHarmonization 3) DeduceRelationship.

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

Generate the UMI count matrix from CEL-Seq2 sequencing data

Brings SingleCellExperiment objects to the tidyverse

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

R/Bioconductor package to interactively explore single cell clusters at multiple resolutions

Label elements within user drawn gates

Clone of the Bioconductor repository for the batchelor package.

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins