Top 20 rna-seq Open-Source Projects

• RNA-seq-analysis

  1 809 0.0 Python

  RNAseq analysis notes from Ming Tang

• rnaseq

  14 780 9.4 Nextflow

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

  

Project mention: R pipelines for bulk RNA-seq analyses | /r/bioinformatics | 2023-12-09

• InfluxDB

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• salmon

  1 728 5.0 C++

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

  

• PyDESeq2

  2 516 8.4 Python

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

  

Project mention: DESeq2 Normalization | /r/bioinformatics | 2023-06-09

https://github.com/owkin/PyDESeq2/blob/main/pydeseq2/preprocessing.py I'm not sure but only a normalized count matrix seems not enough to do differential expression analysis. For example, in this script, it gathers also the size factor from the raw read count matrix. Maybe you could find it somewhere or recalculate it.

• mixcr

  1 310 9.7 Kotlin

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

  

• bambu

  1 163 5.7 R

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

  

• alevin-fry

  3 149 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.

  

• SaaSHub

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• rnaseqc

  1 140 4.5 C++

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

  

• TPMCalculator

  1 122 0.0 C++

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

  

• clustifyr

  1 101 4.9 R

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

  

• 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

  

• diffexpr

  1 68 2.7 Python

  Porting DESeq2 into python via rpy2

• rna-seq-kallisto-sleuth

  1 63 5.9 Python

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

  

• popscle

  1 43 2.7 C++

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

  

• wiggleplotr

  1 33 10.0 R

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

• zarp

  1 29 7.2 Python

  The Zavolab Automated RNA-seq Pipeline (by zavolanlab)

  

Project mention: Any links to R-scripts for common NGS pipelines? | /r/bioinformatics | 2023-05-11

• seq-pipeline

  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.

• 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

• rnaseq

  1 6 3.7 Shell

  RNA-seq analyses. (by davetang)

• SaaSHub

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rna-seq related posts

• 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

• Pipeline to analyze ATAC seq

  3 projects | /r/bioinformatics | 25 Feb 2023
• A note from our sponsor - InfluxDB
  www.influxdata.com | 3 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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