small-rna-seq

A Nextflow pipeline for integrated small RNA-seq and mRNA-seq analysis to uncover exercise-associated miRNA–mRNA regulatory networks.

A rapid and accurate alignment / quantification tool for small non-coding RNAs

End-to-end Snakemake pipeline for miRNA / small RNA-seq: QC, trimming, Bowtie/miRDeep2/miRge3 quantification, DESeq2+edgeR DE, isomiR, multiMiR targets, pathway enrichment, HTML report.