RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
☆1,212Feb 26, 2026Updated this week
Alternatives and similar repositories for rnaseq
Users that are interested in rnaseq are comparing it to the libraries listed below
Sorting:
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆313Feb 25, 2026Updated last week
- Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing☆552Updated this week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,425Updated this week
- ATAC-seq peak-calling and QC analysis pipeline☆220Nov 20, 2025Updated 3 months ago
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆232Nov 21, 2025Updated 3 months ago
- Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…☆1,416May 31, 2023Updated 2 years ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,292Jan 22, 2026Updated last month
- A curated list of nextflow based pipelines☆622Jun 23, 2025Updated 8 months ago
- RNAseq analysis notes from Ming Tang☆1,069Nov 15, 2021Updated 4 years ago
- RNA-seq analysis pipeline for detection of gene-fusions☆171Feb 10, 2026Updated 3 weeks ago
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆189Feb 12, 2026Updated 2 weeks ago
- Pipeline to fetch metadata and raw FastQ files from public databases☆187Feb 8, 2026Updated 3 weeks ago
- Python package with helper tools for the nf-core community.☆293Updated this week
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆862May 29, 2024Updated last year
- RNA-seq aligner☆2,146Mar 18, 2025Updated 11 months ago
- A DSL for data-driven computational pipelines☆3,307Updated this week
- A small-RNA sequencing analysis pipeline☆99Jan 7, 2026Updated last month
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆89Updated this week
- Repository to host tool-specific module files for the Nextflow DSL2 community!☆402Updated this week
- Customizable workflows based on snakemake and python for the analysis of NGS data☆399Jan 23, 2026Updated last month
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,659Feb 15, 2026Updated 2 weeks ago
- A repository for setting up a RNAseq workflow☆454Apr 10, 2017Updated 8 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆826Feb 10, 2026Updated 3 weeks ago
- FlowCraft: a component-based pipeline composer for omics analysis using Nextflow.☆248Aug 10, 2025Updated 6 months ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆561Jan 13, 2026Updated last month
- RNA-seq workflow using STAR and DESeq2☆352Dec 18, 2025Updated 2 months ago
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,025Aug 24, 2024Updated last year
- A curated collection of Nextflow implementation patterns☆368Nov 21, 2023Updated 2 years ago
- R toolkit for single cell genomics☆2,661Feb 20, 2026Updated last week
- rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis☆63Jun 3, 2025Updated 9 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,528Jun 1, 2025Updated 9 months ago
- A list of interesting genome browser and genome visualization programs☆1,051Feb 25, 2026Updated last week
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated 8 months ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,553Dec 11, 2022Updated 3 years ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆262Jul 12, 2025Updated 7 months ago
- Config files used to define parameters specific to compute environments at different Institutions☆107Updated this week
- SRA Tools☆1,309Updated this week
- Make Complex Heatmaps☆1,471Jan 30, 2026Updated last month
- Transcript assembly and quantification for RNA-Seq☆489Dec 26, 2025Updated 2 months ago