Discovering known and novel miRNAs from small RNA sequencing data

Metadata database for ENCODE project

A modular, containerized pipeline for ATAC-seq data processing

snakemake implementation of MoTrPAC RNA-seq pipeline

Scripts to run differential expression analysis using DESeq2 package

RNA-seq aligner

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

bedtools - the swiss army knife for genome arithmetic

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

MACS -- Model-based Analysis of ChIP-Seq

ENCODE ATAC-seq pipeline