Some workflows I wrote for my phd research projects:
- Data pre-processing for variant discovery GATK4
- GATK4 germline short variant discovery (SNPs + Indels)
- GATK4 call somatic snvs indels
- Mitochondrial short variant discovery (SNVs + Indels)
- SV pipelines
- CNV pipelines
- Mutational signatures
- Telomere length estimation
- Eigenetic clock
- Epigenome-wide association study
- Genome-wide association study
- Methylation quantitative trait loci analysis
- Causal mediation analysis
- Create summary stats table
- Chord diagram
- Correlation heatmap
- Heatmap shows overlapping CpGs of epigenetic clocks
- Correlation plots
- Regression coefficient and CI plot
- Meta-analysis funnel plot
- Meta-analysis forest plot
- Sample flow chart
- t-test boxplot
- Bidirectional Manhattan plot and QQ plot
- SNP CpG association
- Global ancestry PCA