For the full list of our labs software, see out GitHub Account. This page highlights databases, software packages, analysis tools, and reusable workflows developed by Boyle Lab members and collaborators.
RegulomeDB annotates variants with functional genomics evidence and predictive models to help interpret non-coding regulatory variation. RegulomeDB v2 added expanded functional genomics data, improved scoring, tissue-aware prediction resources, and visualization support. TURF extends the RegulomeDB framework to prioritize regulatory variants in generic and tissue- or organ-specific contexts, while TLand provides machine-learning models for cell- and organ-specific regulatory variant prioritization.
References: Boyle et al., Genome Research, 2012. Dong et al., Nature Genetics, 2023. Dong and Boyle, Nucleic Acids Research, 2021. Zhao, Dong, and Boyle, bioRxiv, 2023.
The ENCODE Blacklist identifies genomic regions that show anomalous signal across next-generation sequencing experiments. Removing these regions is an important quality-control step for functional genomics analyses, especially ChIP-seq, DNase-seq, ATAC-seq, and related assays.
Reference: Amemiya, Kundaje, and Boyle, Scientific Reports, 2019.
The Boyle Lab developed self-organizing map resources to organize and compare genome-wide regulatory activity across human and mouse tissues and cell types. The SOM Browser provides an interactive web resource for the human-mouse SOM project, and related repositories provide analysis code for the manuscript.
Reference: Diehl et al., Nucleic Acids Research, 2018.
F-Seq is a feature-density estimator for identifying biologically meaningful signal-enriched regions from high-throughput sequencing data. F-Seq2 is a Python rewrite and extension that adds dynamic local statistics, support for common regulatory genomics assays, and IDR-aware peak-calling workflows.
References: Boyle et al., Bioinformatics, 2008. Zhao and Boyle, NAR Genomics and Bioinformatics, 2021.
TRACE is a hidden Markov model for transcription factor footprinting and motif matching using chromatin-accessibility data, including DNase-seq and ATAC-seq. TRACE_GPU accelerates core TRACE computations, including emission-matrix calculation and Viterbi decoding, on GPUs.
Reference: Ouyang and Boyle, Genome Research, 2020.
SNP Effect Matrices model the effect of sequence variants on transcription factor binding affinity. SEMpl is a command-line implementation of the SEM algorithm, SEMplMe incorporates DNA methylation, and SEMPLR provides an R/Bioconductor interface for scoring genomic positions and variants using SEMs.
References: Nishizaki, et al., Bioinformatics, 2019. Nishizaki and Boyle, BMC Bioinformatics, 2022. Kenney et al., Bioinformatics, 2026.
HMMSTR is a modified profile hidden Markov model for determining tandem-repeat copy number from raw long-read sequencing data. It is optimized for targeted sequencing experiments.
Reference: Van Deynze et al., Nucleic Acids Research, 2025.
OnRamp is a bulk plasmid sequencing tool that streamlines pooled plasmid validation. The Boyle Lab repository provides the web-enabled version, and the command-line workflow is available through the associated bulkPlasmidSeq codebase.
Reference: Mumm et al., Genome Research, 2023.
NanoPal and associated Cas9 targeted enrichment pipelines support long-read enrichment and analysis of mobile-element insertions. The repository includes workflows for L1Hs, AluYb, AluYa, SVA_F, and SVA_E mobile-element families, plus guide-RNA design, cleavage-site analysis, and methylation analysis scripts.
Reference: McDonald et al., Nature Communications, 2021.
Minimera detects foldback chimeras in Oxford Nanopore sequencing data using minimizers and is released as command-line binaries and Singularity containers.
