Top 21 rna-seq Open-Source Projects

1. rnaseq

   1 14 1,016 9.7 Nextflow

   RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

   

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3. RNA-seq-analysis

   2 1 976 0.0 Python

   RNAseq analysis notes from Ming Tang

   

4. salmon

   3 1 802 4.1 C++

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

   

5. PyDESeq2

   4 2 643 8.4 Python

   A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

   

6. mixcr

   5 1 350 9.0 Kotlin

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

   

7. bambu

   6 1 206 6.5 R

   Reference-guided transcript discovery and quantification for long read RNA-Seq data

   

8. alevin-fry

   7 3 182 7.9 Rust

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

   

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10. rnaseqc

    8 1 161 5.0 C++

    Fast, efficient RNA-Seq metrics for quality control and process optimization

    

11. ceLLama

    9 1 147 7.6 R

    Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

    

    Project mention: Show HN: CeLLama – Single cell annotation with local Large Language Models | news.ycombinator.com | 2024-07-28

12. TPMCalculator

    10 1 129 3.6 C++

    TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

    

13. clustifyr

    11 1 121 6.0 R

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

    

14. COVID-19-RNA-Seq-datasets

    12 3 78 3.8 Python

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

    

15. cellSNP

    13 2 77 0.0 Python

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

    

16. rna-seq-kallisto-sleuth

    14 1 68 8.0 Python

    A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

    

17. diffexpr

    15 1 68 2.7 Python

    Porting DESeq2 into python via rpy2

    

18. popscle

    16 1 46 2.7 C++

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

    

19. wiggleplotr

    17 1 37 10.0 R

    A small R package to make sequencing read coverage plots in R.

    

20. zarp

    18 1 35 4.8 Python

    The Zavolab Automated RNA-seq Pipeline (by zavolanlab)

    

21. gEAR

    19 1 15 9.8 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)

    

22. seq-pipeline

    20 1 10 4.6 PHP

    Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

    

23. rnaseq

    21 1 9 8.5 Shell

    RNA-seq analyses. (by davetang)

    

24. InfluxDB

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    InfluxDB high-performance time series database. Collect, organize, and act on massive volumes of high-resolution data to power real-time intelligent systems.

    

rna-seq related posts

• Show HN: CeLLama – Single cell annotation with local Large Language Models

  2 projects | news.ycombinator.com | 28 Jul 2024

• DESeq2 Normalization

  1 project | /r/bioinformatics | 9 Jun 2023

• Point of using Hisat2 build to index reference genomes when working with known genomes mouse/human?

  1 project | /r/bioinformatics | 29 May 2023

• I used featureCounts to quantify RNA-seq reads and got a low successful alignment percentage. Is this a problem?

  1 project | /r/bioinformatics | 18 May 2023

• Any links to R-scripts for common NGS pipelines?

  2 projects | /r/bioinformatics | 11 May 2023

• How to create VCFs for scRNA-Seq data sets

  1 project | /r/bioinformatics | 16 Mar 2023

• How to know where to align if I have RNAseq data??

  1 project | /r/bioinformatics | 9 Mar 2023
• A note from our sponsor - CodeRabbit
  coderabbit.ai | 26 Apr 2025

  Revolutionize your code reviews with AI. CodeRabbit offers PR summaries, code walkthroughs, 1-click suggestions, and AST-based analysis. Boost productivity and code quality across all major languages with each PR. Learn more →

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