A Minimal Book Example
1
Prerequisites
2
Analyis of new generation sequencing data in R
2.1
Get fastq from SRA
3
Get fastq from SRA database
3.1
Get fastq from SRA database
4
Differential expression analysis using basic R
4.1
Gene expression analysis of histone deacetylase 1 (HDAC1) knockout mouse.
4.2
Sources
5
Genome Wide Associated Studies (GWAS)"
5.1
SNP analysis using SNPasoc R package
5.2
GWAS using PLINK
6
Hi-C workflow
6.1
Using straw tool to extract contact matrix from .hic files
6.2
HiC-Pro pipeline
6.3
multiHiC compare for compare of 2 Hi-C datasets (Rao et al. 2017)
6.4
Joint normalization of Hi-C
6.5
Difference detection
Published with bookdown
A Minimal Book Example
Chapter 2
Analyis of new generation sequencing data in R
2.1
Get fastq from SRA