RNA-seq co-expression

February 10, 2023

  1. coseq: Co-expression analysis of sequencing data πŸ”—
  2. ICAL: Model selection for model based clustering of annotated data πŸ”—
  3. HTSCluster: Clustering high-throughput sequencing data with Poisson mixture models πŸ”—
  1. Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2018) Clustering transformed compositional data using K-means, with applications in gene expression and bicycle sharing system data. Journal of Applied Statistics, 46(1):47-65. πŸ”— πŸ“„ πŸ”„ πŸ’»

  2. Rau, A. and Maugis-Rabusseau, C. (2018) Transformation and model choice for RNA-seq co-expression analysis. Briefings in Bioinformatics, bbw128. πŸ”— πŸ“„ πŸ”„ πŸ’»

  3. Mondet, F., Rau, A., Klopp, C., Rohmer, M. Severac, D., Le Conte, Y., and Alaux, C. (2018) Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. BMC Genomics, 19:328. πŸ”— πŸ“„

  4. Sauvage, C., Rau, A., Aichholz, C., Chadoeuf, J., Sarah, G., Ruiz, M., Santoni, S., Causse, M., David, J., GlΓ©min, S. (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. The Plant Journal, 91(4):631-645. πŸ”— πŸ“„

  5. Gallopin, M., Celeux, G., JaffrΓ©zic, F., Rau, A. (2015) A model selection criterion for model-based clustering of annotated gene expression data. Statistical Applications in Genetics and Molecular Biology, 14(5): 413-428. πŸ”— πŸ“„ πŸ”’

  6. Rau, A., Maugis-Rabusseau, C., Martin-Magniette, M.-L., Celeux, G. (2015) Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. Bioinformatics, 31(9): 1420-1427. πŸ”— πŸ“„ πŸ”„ πŸ’»

Posted on:
February 10, 2023
2 minute read, 224 words
See Also:
Network inference
Multi-omic data integration
Applications in animal, plant, and human genomics