Top 17 single-cell Open-Source Projects

• awesome-single-cell

  3 2,918 5.2

  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

• salmon

  1 731 5.0 C++

  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment (by COMBINE-lab)

  

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• dance

  1 323 8.7 Python

  DANCE: a deep learning library and benchmark platform for single-cell analysis (by OmicsML)

  

• mixcr

  1 310 9.7 Kotlin

  MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

  

• scarches

  1 310 6.9 Jupyter Notebook

  Reference mapping for single-cell genomics

  

• octopus

  1 296 4.0 C++

  Bayesian haplotype-based mutation calling (by luntergroup)

  

• pagoda2

  2 191 5.3 JavaScript

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

  

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

• alevin-fry

  3 152 7.2 Rust

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

  

• scDblFinder

  1 131 6.7 R

  Methods for detecting doublets in single-cell sequencing data

• cellsnp-lite

  1 117 7.1 C

  Efficient genotyping bi-allelic SNPs on single cells

  

• too-many-cells

  0 100 4.5 Haskell

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

• COVID-19-RNA-Seq-datasets

  3 75 3.8 Python

  A repository for sharing information on available COVID-19 RNA-Seq datasets

• cellSNP

  2 69 0.0 Python

  Pileup biallelic SNPs from single-cell and bulk RNA-seq data

  

• scAge

  1 33 0.0 Jupyter Notebook

  Profiling epigenetic age in single cells

• FastIntegration

  1 21 0.0 R

  FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis

  

• gEAR

  1 10 8.3 Jupyter Notebook

  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. (by IGS)

  

Project mention: How can I read single cell data into scanpy? txt files | /r/bioinformatics | 2023-06-23

• seurat-docker

  1 4 0.0 Dockerfile

  Docker images of Seurat

  

• SaaSHub

  www.saashub.com featured

  SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

  

single-cell related posts

• How to create VCFs for scRNA-Seq data sets

  1 project | /r/bioinformatics | 16 Mar 2023

• RNA VELOCITY

  2 projects | /r/bioinformatics | 1 Dec 2022

• GOterm analysis in Seurat

  1 project | /r/bioinformatics | 6 Aug 2022

• "Surpassing" Go & the near-future of Rust: in what domains will Rust succeed?

  2 projects | /r/rust | 3 Apr 2022

• Researchers Introduce Single-Cell Architecture Surgery (scArches), A Deep Learning Strategy For Mapping Single-Cell Data to Reference Atlases

  1 project | /r/artificial | 2 Sep 2021

• Annotating variants in single-cell sequencing data

  1 project | /r/bioinformatics | 13 Mar 2021

• Seurat Vs Pagoda2 For Scrnaseq Analysis

  1 project | /r/bioinformatics | 4 Jan 2021
• A note from our sponsor - InfluxDB
  www.influxdata.com | 5 May 2024

  Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality. Learn more →

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