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

Nextflow 954 716 Updated Jan 8, 2025

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Nextflow 26 15 Updated Jan 2, 2022
Nextflow 12 5 Updated Oct 31, 2020

A nextflow pipeline for processing sc-RNASeq data, performing QC and integration and preparing the results for further investigation using cellxgene.

Nextflow 9 Updated Jun 30, 2024