bixBeta / TReX Star 4 Code Issues Pull requests RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @cornell-TREX ggplot2 shiny rnaseq multiqc star bash-script shiny-apps bash-scripting 10xgenomics singlecell smallrna mirdeep2 scrna smallrna-seq seurat Updated Mar 27, 2024 Shell
TejusK123 / AutoDeep Star 4 Code Issues Pull requests Simple downstream stratification of miRDeep2 outputs via XGBoost supervised-learning user-friendly mirdeep2 xgboost-classifier mirna-curation Updated Mar 3, 2026 Python
OpenOmics / mir-seek Star 2 Code Issues Pull requests An awesome microRNA-sequencing pipeline snakemake singularity mirna mirdeep2 mirna-seq micro-rna micro-rna-expression mature-mirna Updated Dec 15, 2025 Python
Brochado-Kith / MicroRNA_pipeline Star 2 Code Issues Pull requests This is a pipeline for microRNA extraction from raw sequences shell mapping slurm human trimming bash-script raw-data mirdeep2 quantifying mirnas microarns Updated Mar 6, 2024 Shell
Drmirdeep / mirdeep2_patch Star 1 Code Issues Pull requests Discovering known and novel miRNAs from small RNA sequencing data - updated scripts before release data analysis mapping sequencing prediction small rna patch quantification mirna smallrna mirdeep microrna mirdeep2 Updated Oct 8, 2021 Perl
challagandla / oracle-mirna-seq Star 1 Code Issues Pull requests 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. bioinformatics snakemake genomics computational-biology deseq2 differential-expression edger mirna mirdeep2 small-rna-seq isomir Updated Jul 15, 2026 R