Hespresso
Statistical test for detecting shifts in homeolog expression ratios in allopolyploids
Install / Use
/learn @bitdessin/HespressoREADME
hespresso: LRT for Detecting Shifts in Homeolog Expression Ratios from Allopolyploid RNA-seq Data
hespresso blends homeolog expression with espresso, capturing the essence of power, energy, and focus in homeolog expression analysis. It provides statistical tests for detecting shifts in homeolog expression ratios among subgenomes of allopolyploid species across diverse conditions, using RNA-seq read count data. Take a sip of hespresso, and start your analysis strong!
Documentation
- https://bitdessin.github.io/hespresso/
Citations
If you use HOBIT, please cite:
Sun J, Sese J, Shimizu KK. A likelihood ratio test for detecting shifts in homeolog expression ratios in allopolyploids. New Phytol., 249(1):603-617, 2026. 10.1111/nph.70648
If you use HomeoRoq, please cite:
Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J. Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis. Nucleic Acids Res. 42(6):e46, 2014. 10.1093/nar/gkt1376
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