Tools

These research tools and web apps support exploration of genomic and epigenomic datasets from collaborative projects.

Human Imprintome methylation browser view showing ICR methylation points across genomic tracks

Research Web App

Human Imprintome

A searchable browser for human imprint control regions (ICRs), including somatic and gametic methylation datasets, gene and coordinate search, and CpG methylation visualization.

Related paper: Jima DD, Skaar DA, Planchart A, et al. 2022. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 17(13):1920-1943. doi:10.1080/15592294.2022.2091815.

Project Site PubMed
Horizontal temposeqcount pipeline diagram from FASTQ inputs through probe mapping, count formatting, count combining, alignment summary, and plots

Bioinformatics Pipeline

temposeqcount

An analysis pipeline for TempO-Seq/RASL-Seq projects that accepts demultiplexed FASTQ files and a probe/sample manifest, then quantifies reads mapped to probes per well in parallel.

Related paper: House JS, Grimm FA, Jima DD, Zhou Y-H, Rusyn I, Wright FA. 2017. A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics. Frontiers in Genetics 8:168. doi:10.3389/fgene.2017.00168.

GitHub Repository PubMed
ECBC and USAMRIID-WRAIR pathogen detection pipeline workflow for sequencing data processing, host removal, assembly, taxonomy clustering, and reference mapping

Legacy Platform

Pathosphere.org / ECBC Pipeline

A web-based, open-source informatics platform for pathogen detection and characterization from next-generation sequencing data, including workflows for host removal, de novo assembly, taxonomy clustering, reference mapping, and nearest-neighbor identification.

Related paper: Kilianski A, Carcel P, Yao S, et al. 2015. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics 16:416. doi:10.1186/s12859-015-0840-5.

Article PubMed