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Genotyping, GWAS and genomic selection data Données génotypage, GWAS et sélection génomique
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Dec 8, 2020 - ThaliaDB maize Dataverse
Nicolas, Stéphane; Madur, Delphine; Charcosset, Alain; Bauland, Cyril; Combes, Valérie; Berard, Aurélie; Arca, Mariangela; Mary-Huard, Tristan; Le Paslier, Marie-Christine; Gouesnard, Brigitte, 2020, "Fluorescence intensity datasets and R scripts to predict allelic frequencies in DNA bulks using maize 50K Illumina array", https://doi.org/10.15454/GANJ7J, Portail Data INRAE, V1, UNF:6:IvZiMGs4Oo8oWZqgBbcDdA== [fileUNF]
R scripts and fluorescence intensity datasets of 24 controlled pools and 327 inbred lines panels extracted from 50K Illumina Infinium HD array (Ganal et al., 2010). These datasets and R scripts can be used to calibrate a model to predict allelic frequencies in new DNA bulks using...
text/tsv - 683.5 MB - MD5: adc4fcb77ad9e62231a3fe1d07e116f4
Training set with fluorescence intensity ratios (FIR) for 327 inbred lines on 32,788 prefixed PZE SNPs from 50K maize Illumina Array, used to test allele fixation in DNA bulks of landraces. Table display 5 columns: "ID.Genotypage", "SNP.Name",""Cas"","Attendu","RatioObs" These 5...
text/tab-separated-values - 1.3 MB - MD5: 3cfd55062ca797a3e6109a8270a42380
Training set of 1,000 SNPs and 24 controlled pools used to predict allelic frequencies for polymorphic SNPs using a common logistic regression after testing for fixation of alleles. Table have 4 columns with the following headers: "SNP.Name","Sample.ID","RatioObs","Attendu". Thes...
text/tab-separated-values - 40.3 MB - MD5: 4bc959b9571abdab7b789e0291fb3402
Fluorescence Intensity Ratios for 32,788 SNPs on 20 samples corresponding to 10 duplicated landraces. This table has 5 columns with headers as follows: "SNP.Name","Sample.name","X","Y", "RatioObs". These columns correspond to name of SNP, name of sample, fluorescence in...
text/x-r-source - 32.8 KB - MD5: 60ae0e0796cfd3f031c5f13ec84a2356
Functions to predict allelic frequencies using a two-step approache and to visualize prediction: Test of allele fixation, then logistic regression for polymorphic SNPs.
text/x-r-source - 6.0 KB - MD5: 90e666cd6d8619a15288e93046d9b58b
- R scripts (Pipeline) that apply R functions (04_Function_PredAllFreqInDNABulk_Publi.R) to two training datasets corresponding to fluorescence intensity data of 327 lines (1_Train_set_327lines_32788SNP.tsv ) and two series of controlled pools (2_Train_set_24pools_TF_1000SNP.tab)...
Feb 7, 2020 - ThaliaDB maize Dataverse
Rio Simon, 2020, "FlintDent GWAS dataset", https://doi.org/10.15454/OQT5CY, Portail Data INRAE, V1
This dataset corresponds to the data associated with the study: "Disentangling group specific QTL allele effects from genetic background epistasis in GWAS: an application to maize flowering" by Rio et al. (2019). The data includes genotypic and phenotypic information for a panel...
Feb 7, 2020 - FlintDent GWAS dataset
text/csv - 898.4 MB - MD5: 12ff7a95cb6b6ef2a14a7d33e82e4e56
Matrix (970 lines x 482078 SNPs) indicating the ancestry of each allele (0: flint genetic group, 1: dent genetic group)
Feb 7, 2020 - FlintDent GWAS dataset
text/csv - 19.5 KB - MD5: 4c4f4f3dcc5c2ac1e8004e31ac4d817f
Data.frame (970 lines x 1 genetic background) indicating the genetic background of the line (Dent, Flint or Admixed)
Feb 7, 2020 - FlintDent GWAS dataset
text/csv - 898.4 MB - MD5: 4058490721c4a281f42ad1e0c1bfab11
Genotyping matrix (970 lines x 482078 SNPs) with bi-allelic genotypic scores of each homozygous inbred line (coded 0/1)
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