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rna-seq

Here are 1,667 public repositories matching this topic...

nf-core / rnaseq

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

workflow rna-seq pipeline nextflow rna nf-core

Updated Jul 16, 2026
Nextflow

theislab / single-cell-best-practices

https://www.sc-best-practices.org

tutorial rna-seq book single-cell

Updated Jul 18, 2026
Jupyter Notebook

scverse / gget

🧬 gget enables efficient querying of genomic reference databases

rna-seq genomics reference databases ensembl proteomics blast transcriptomics uniprot ncbi enrichment-analysis enrichr cellxgene alphafold gget archs4 alphafold2

Updated Jul 16, 2026
Python

crazyhottommy / RNA-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Updated Nov 15, 2021
Python

COMBINE-lab / salmon

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

c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish single-cell-rna-seq selective-alignment rna-seq-quantification

Updated Jul 17, 2026
Rust

pachterlab / kallisto

Near-optimal RNA-Seq quantification

rna-seq kallisto pseudoalignment

Updated Jul 12, 2026
C

deeptools / deepTools

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

Updated Jul 18, 2026
Python

scverse / PyDESeq2

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

python bioinformatics rna-seq transcriptomics differential-expression

Updated Jul 13, 2026
Python

saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells

rna-seq gene-expression network-inference data-integration single-cell-rna-seq single-cell-omics intercellular-communication ligand-receptor ligand-target cell-cell-communication

Updated Jun 1, 2026
R

twbattaglia / RNAseq-workflow

A repository for setting up a RNAseq workflow

science workflow bioinformatics rna-seq pipeline sequencing genes

Updated Apr 10, 2017
R

agitter / single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

bioinformatics rna-seq single-cell pseudotime-algorithms

Updated Apr 28, 2026

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

workflow rna-seq snakemake ngs hi-c chip-seq atac-seq bisulfite-sequencing

Updated Jul 13, 2026
Python

milaboratory / mixcr

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

bioinformatics rna-seq sequencing immunology t-cell antibody t-cell-receptor rep-seq single-cell 10x

Updated Jul 10, 2026
Kotlin

kpatel427 / YouTubeTutorials

youtube bioinformatics rna-seq tutorials single-cell bioinformatics-analysis

Updated Oct 1, 2024
R

scRNA-tools / scRNA-tools

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

rna-seq database tools software scrna-seq single-cell single-cell-rna-seq

Updated Jul 19, 2026
R

nf-core / scrnaseq

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools alevin cellranger star-solo

Updated Jul 13, 2026
Nextflow

pachterlab / sleuth

Differential analysis of RNA-Seq

rna-seq

Updated May 28, 2025
R

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

rna-seq pipeline expression rnaseq umi single-cell fastq barcodes dge

Updated Jul 12, 2024
R

GoekeLab / bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

workflow bioinformatics rna-seq pipeline workflow-management bioinformatics-workflows

Updated Oct 27, 2021
Python

jaechang-hits / SciAgent-Skills

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.

Updated Jun 15, 2026
Python

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