Indices and tables

CIPHER is a workflow platform written in the Nextflow DSL that was developed to enhance reproducibility among research, and to simplify data processing for non-computational scientists. CIPHER can be used for the efficient pre-processing and analysis of high-throughput sequencing data including: ChIP-seq, RNA-seq, DNase-seq, MNase-seq, GRO-seq, and ATAC-seq.

For support, questions, or feature requests contact: or submit an issue at our github.

CIPHER is run from the command line, can be run on a local desktop or HPC and only requires the installation of Nextflow and Docker (optionally). Please visit the ‘Installation’ page for more details.