Codes used to study the Crassostrea gigas oyster transcriptome response to Alexandrium exposure

• Main Author: Mat, Audrey
• Format: Dataset
• Language: unknown
• Published: SEANOE 2018
• Subjects: Crassostrea gigas; Alexandrium minutum; Paralytic Shellfish Toxins; R; Transcriptomic; Differential expression; Elastic-net regression; Script
• Online Access: https://doi.org/10.17882/52864

R scripts written for differential analysis and regression analysis to investigate the molecular basis of Paralytic Shellfish Toxins load in the oyster Crassostrea gigas exposed to the toxigenic alga Alexandrium minutum. Differentially expressed genes were analyzed with R (version 3.2.3, Gentry et al. (2004) Genome Biol 5:R80) using the packages DESeq2 (version 1.10.0; Love et al. (2014) Genome Biol 15:1-21) and edgeR (version 3.12.0, Robinson et al. (2010) Bioinformatics 26:139-140). Elastic-net regression was run with R using the package glmnet (version 2.0-2, Friedman et al. (2010) J Stat Softw 33:1-22).