R code associated with the switchgrass genome paper. Includes 1) R code to run the neural network to assign switchgrass ecotypes, 2) R code to conduct discriminant analysis of principle components for switchgrass ecotypes, 3) R code to run genome-wide association and multivariate adaptive shrinkage for the switchgrass diversity panels, and 4) R code to calculate trait heritabilities and conduct regional heritability mapping.
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Replication Data for: Switchgrass Phenology Paper
Sep 3, 2021
MacQueen, Alice, 2021, "Replication Data for: Switchgrass Phenology Paper", https://doi.org/10.18738/T8/A604BU, Texas Data Repository, V1
SNP data used for genome-wide association in the switchgrass phenology paper. SNP data includes three sets of three SNP files (with the same filename, and .bed, .bim, and .fam file extensions): genetic data for the Midwest genetic subpopulation, the Gulf genetic subpopulation, an...
SNP and Annotation Data for Switchgrass genome paper
Jan 7, 2021
MacQueen, Alice, 2021, "SNP and Annotation Data for Switchgrass genome paper", https://doi.org/10.18738/T8/ET9UAU, Texas Data Repository, V1
SNP data used for genome-wide association in the switchgrass genome paper. SNP data includes five sets of three SNP files (with the same filename, and .bed, .bim, and .fam file extensions), and two annotation data files.
Replication Data for: Switchgrass Genome Paper
Dec 13, 2020
Lovell, John; MacQueen, Alice; Napier, Joe, 2020, "Replication Data for: Switchgrass Genome Paper", https://doi.org/10.18738/T8/J377KE, Texas Data Repository, V1
R script containing the code to replicate the results of the switchgrass genome paper. Includes code to: a) run the neural network to assign ecotypes to switchgrass individuals, identified by PLANT_ID's (six character strings that typically begin with J), based on individuals wit...
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