OUTLINE

Genotype preparation

1. Sequencing
2. Imputation
3. QC（call rate, MAF）
4. Cluster analysis [code]
5. 其他比对 SV、CNV

Phenotype preparation

1. BLUP

Basic statistics

1. Distrubution
   zscore(Normalization or Standardization)
2. Corelate
   (pearson,spearman,kendall,
   fisher,chip-squared test)
3. Linear algebra ……
4. Bayesian
5. probability and Likelihood
6. Least squares method …… —> statistics
7. How to calculate 'r2'?
   LD function(LDSC)
8. Bonferroni

GWAS

1. kinship
   How to deal with population strucure?
   （Phylogenetic tree）
2. GWAS model
3. What are lambda, P, PVE, effect size?
4. How to pick 'p threshold'?
   (how to calculate independent snp?)
5. Fine mapping
   conditional analysis [code]
6. LD block
   locus zoom [code]

others

BSA analysis
trio-GWAS
haplotype analysis
PRS

GS

1. GS model
2. Genomic prediction(G matrix) [code]
   Prediction acuracy(cross validation) [code]

sQTL

Instrument（leafcutter踩坑指南）

post-analysis

7. Heritability
8. SNP annotation [code]
9. neutrality tests

Integrative analysis

1. Colocalization
   共定位 [code]
2. MR [code]

TWAS

1. TWAS model [code]

Meta-analysis

1. Merge different Genotype [code]

Analysis about DNA

ATAC-seq [code]

1. Chrom accessibility region(where, function)
2. Method

Bisfule-seq [code]

1. Method
2. DMR [code]

DAP-seq

RNA-seq [code]

https://ming-lian.github.io/2019/02/08/Stat-on-RNAseq/
1.Sequencing(depth,coverage,library)
https://www.jieandze1314.com/post/cnposts/239/
批次效应 batch
2.How to aligh
3.Flow and note

Find DEG [code]

R package: Deseq principles

WGCNA [code]

Interpreting literature：

Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding - ScienceDirect
Open problems in human trait genetics | Genome Biology
GTEX

Book to read

Likelihood
算法设计与分析基础_第3版
机器学习周志华

学习思路

statistics -> data science
quantitative genetics

Algorithm & Programming

Makefile
R packages: ggplot