idHX

idHX is a bioinformatics tool designed for the rapid identification of highly expressed genes from RNA‑sequencing datasets. The software was first released by the Genomics Research Group at the University of Riverdale in 2012, and has since been adopted by laboratories worldwide for both academic research and pharmaceutical development.

The core of idHX is a statistical ranking algorithm that normalizes read counts, corrects for library size bias, and applies a variance‑stabilizing transformation to produce robust expression scores. Users provide raw FASTQ files or processed count matrices, and idHX outputs a ranked list of genes with accompanying metrics such as fold change and false discovery rate. The tool also includes optional modules for pathway enrichment analysis and visualization of expression heatmaps.

idHX has been cited in over 120 peer‑reviewed publications by 2023, particularly in studies of plant stress responses, cancer transcriptomics, and pathogen–host interaction analyses. Its open‑source implementation under a permissive MIT license encourages community contributions and the development of plugins for specific organism genomes.

The software is available for Windows, macOS, and Linux, and is distributed as a command‑line package along with Docker containers for containerised deployments. Documentation is maintained on a web portal that includes tutorials, FAQs, and a user forum.

References

1. Walker, J. et al. “idHX: Fast Identification of Highly Expressed Genes.” *Genome Res.* 2015;25(4):570‑579.

2. Patel, S. & Chong, M. “Applications of idHX in Cancer Genomics.” *J. Comput. Biol.* 2018;25(6):743‑751.