- Unique identifier:
- Software type:
- Restrictions to use:
- Input format:
- Computer skills:
- STAR, Samtools, R-package locfit (used in “calcpval_one.R”), R-package doMC (used in “calcpval_one.R”)
- Homeolog Ratio and Quantification
- Command line interface
- Input data:
- Parental genomic sequences [Parent1_genome.fas] and [Parent2_genome.fas] and RNA-seq reads (paired-end), 6 libraries.
- Operating system:
- Documentation: http://seselab.org/homeoroq/homeoroq_procedures_131011.pdf
- Jun Sese <>
- Kentaro Shimizu <>
- Satoru Akama <>
No open topic.
(Akama et al., 2014)
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis.
Nucleic Acids Res.
PMID: 24423873 DOI: 10.1093/nar/gkt1376
Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan; Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Zurich, Switzerland
Supported by Young Investigator Award of Human Frontier Science Program; Marie Heim-Vogtlin grant of the Swiss National Science Foundation (SNF) and Forschungskredit of University of Zurich; the University Research Priority Programs of Evolution in Action of the University of Zurich and of Systems
Biology/Functional Genomics; JSPS KAKENHI [23128504, 24651227 and 24680032] and Grant-in-Aid for Scientific Research on Innovative Area "Genome Science", Ministry of Education, Culture, Sports, Science and Technology in Japan.
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