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Project Introduction
Sample Information and Record of Technical Variables
RNA-seq Data
Methylation Data
Differentiatlly methylated regions
Integration of gene expression levels and methylatiom levels: humans and chimpanzees
Effect size estimation
Notes

Last updated: 2017-12-30

Code version: f7fdda039d107469215eb81acc8db36ff28aed88

Project Introduction

Sample Information and Record of Technical Variables

Technical variables documented/tested (sample information, RNA-seq, BS-seq, QC, processing, etc.)

RNA-seq Data

Pre-processing

Unmapped and Mapped Reads

Normalization

Analysis with Technical Factors

Final filtering, normalizations, and analysis with technical factors (12,184 genes)

Processing using filtering with lowly expressed genes

Univariate analysis on gene expression

Methylation Data

Human-chimpanzee orthologous promoters
Human-chimpanzee-rhesus orthologous promoters
Clustering after testing for technical variables
tissue DMRs

Differentiatlly methylated regions

Integration of gene expression levels and methylatiom levels: humans and chimpanzees

Inter-species and inter-tissue example with FSR

Effect size estimation

Notes

RNA-seq Normalization Notes