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71 to 80 of 101 Results

S3_GeneticDiversity.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 8.0 MB - MD5: b221ac40593882f7deb0a1a3d35b3a17 Documentation Introduction to Population Genetics for analysing the genetic diversity of crops
S3_Genetic_diversity+structure.html May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) HTML - 4.3 MB - MD5: 828d31d700d62f10b8f9fbf120f7883a CodeDocumentation In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packa...
S3_install.packages.R May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) R Syntax - 975 B - MD5: c7a6dda8fc71fd10aebe8212eb9edbdf Code List of packages to install for session 3 on diversity and structure analysis. To be opened with RStudio.
S3_Structure.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 3.8 MB - MD5: f5d2b43e2d5a5eefd051c29b2c68833e Documentation Introduction to Population Genetics for analysing the genetic structure of crops.
S4_Introduction_GenomeWideAssociationStudy_GWAS.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 912.5 KB - MD5: da9c01bfb9ae62fefc2a5b288cc9889d Documentation Introduction to the core concept of genome wide association studies.
S4_script_GWAS_basic_Rcode.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 73.2 KB - MD5: 17bd3bb83031e7349c5d4730581569e8 Documentation This file comments on the R script for GWAS analysis.
S4_Script_GWAS_Introduction.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 574.9 KB - MD5: b3bd4b806a6968e50f665cd4e34e832b Documentation This file presents a script for GWAS analysis using R. We used a dataset of pearl millet accessions (Varshney et al. 2017).
sample_metadata.tab May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Tabular Data - 2.5 KB - 5 Variables, 55 Observations - UNF:6:LNg1C4IBq05VUN9bbZDOeQ== Data Table containing the passport data of the pearl millet accessions. This data file is associated with the script "S1_Introduction_to_R_Passport.html". These data are published in Berthouly-Salazar et al. (2016).
DiscriminantSitesOnly_biallelic_freebayes_bcftools_snps_on_AZUwithOrganelles_chr01.vcf.gz Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Gzip Archive - 206.7 MB - MD5: 161bb7f90f38757bd830bc5e005cd453 Data Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population
ReadMe.txt Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Plain Text - 1.0 KB - MD5: 91fe283277eff5f80f7fb8e3703d8c40 Documentation ReadMe file - data citation, description and terms of use.

S3_GeneticDiversity.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 8.0 MB -

Documentation

Introduction to Population Genetics for analysing the genetic diversity of crops

S3_Genetic_diversity+structure.html

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

HTML - 4.3 MB -

CodeDocumentation

In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packa...

S3_install.packages.R

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

R Syntax - 975 B -

Code

List of packages to install for session 3 on diversity and structure analysis. To be opened with RStudio.

S3_Structure.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 3.8 MB -

Documentation

Introduction to Population Genetics for analysing the genetic structure of crops.

S4_Introduction_GenomeWideAssociationStudy_GWAS.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 912.5 KB -

Documentation

Introduction to the core concept of genome wide association studies.

S4_script_GWAS_basic_Rcode.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 73.2 KB -

Documentation

This file comments on the R script for GWAS analysis.

S4_Script_GWAS_Introduction.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 574.9 KB -

Documentation

This file presents a script for GWAS analysis using R. We used a dataset of pearl millet accessions (Varshney et al. 2017).

sample_metadata.tab

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Tabular Data - 2.5 KB - 5 Variables, 55 Observations -

Data

Table containing the passport data of the pearl millet accessions. This data file is associated with the script "S1_Introduction_to_R_Passport.html". These data are published in Berthouly-Salazar et al. (2016).

DiscriminantSitesOnly_biallelic_freebayes_bcftools_snps_on_AZUwithOrganelles_chr01.vcf.gz

Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Gzip Archive - 206.7 MB -

Data

Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

ReadMe.txt

Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Plain Text - 1.0 KB -

Documentation

ReadMe file - data citation, description and terms of use.

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