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User Guide for ShiNyP: SNP Analysis and Visualization Platform

9 FAQ

Index

  • AI Report 8

  • AMOVA (Analysis of MOlecular VAriance) 5.4

  • API key 8

  • Bayesian Information Criterion (BIC) 4.2

  • Chromosome Info. 2.3 5.2 6.3 6.4 7.2

  • Circos Plot 5.2

  • Core Sample Set 7.1

  • Core SNP Set 7.2

  • DAPC (Discriminant Analysis of Principal Components) 4.2

  • data.frame 1.1

  • Demo Data 1.1

  • Diversity Parameter 5.1

  • Genetic Distance 5.3

  • genind 3

  • genlight 5

  • Group Info. 3 4.5 4.6 5.1 6.2

  • Hardy-Weinberg equilibrium (HWE) 2.2

  • Heterozygosity rate 2.1

  • IBS (Identity By State) 6.3

  • Kinship Analysis 4.5

  • Manhattan Plot 6.4

  • Minor allele frequency (MAF) 2.2

  • Missing rate 2.1

  • NJ (Neighbor-Joining) Tree 4.4

  • OutFLANK 6.2

  • PCA (Principal Component Analysis) 4.1

  • pcadapt 6.1

  • Permutation Test 5.4

  • Sample QC 2.1

  • Scatter Plot 4.6

  • ShiNyP ShiNyP

  • Site Info. 1.1 2.1 2.2 2.3 5.1 6.1 6.2 6.3 7.2

  • SNP Density 2.3

  • SNP QC 2.2

  • Tree Plot 4.7

  • UPGMA (Unweighted Pair Group Method with Arithmetic mean) Tree 4.3

  • VCF 1.1

Bibliography

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