Embedded Files
* Figures presented here are selected ones from the results I have produced myself.
An alluvial plot showing CAR-T cell lineages over time
An UMAP plot of CAR-T cells
and some interesting lineages by arrow
A dot plot to show expression changes among pseudo-time states
A pseudo-time analysis result of single cell data using Monocle
An alluvial plot to show how lineages are linked between GMP and Post-Infusion cells
A Kolmogorov–Smirnov test result
A heatmap of differentially expressed genes
A scatter plot that shows correlation between two VIPER enrichment scores
I developed a Java application with User Interface that can import gene expression data and can do various analyses
A world disease map created based on disease-location associations from Web Crawl Data
I predicted ethnicity of TCGA COAD/READ samples by using race info of 1000 Genomes Project. The PCA plots are based on genotype data
A circular plot that shows relations among variables
A PCA plot of samples labeled with cell line info
A differential expression result by using limma-voom on RNA-Seq data
A differential methylation result by using ChAMP package of R
A beeswarm (box) plots that compare MCP-Counter Scores among different groups in each cell type
A network presentation to find meaningful modules by using RedeR package of R
A hierarchical clustering and MDS plots of 36 normal (GTEx) and 26 cancer (TCGA) tissues
based on their VIPER enrichment profiles
Master regulator analysis result (VIPER)
Correlations between gene expression levels and methylation levels of some important genes
Survival analysis result of different groups (a Kaplan–Meier plot and a beewarm plot of survival (months) differences)
Demographic presentations of the TCGA COAD/READ samples
Consecutive bar plots that show difference in mapped reads (RNA-Seq) between two groups of the 214 precursor loci
A network graph of disease-chemical compound associations drawn by Cytoscape
ROC curves of many classification methods (caret of R)
The top differentially methylated region derived by DMRcate package of R
A pathway analysis result with Pathview package of R (KEGG database)
MySQL workbench example, SQL querying, and the result table in my local computer
A somatic mutation data summary plot by using maftools package of R
A FastQC result of base quality scores of a Bam file
A volcano plot based on a differential expression result
A TF foot-printing analysis result from ATAC-Seq by using TFBSTools package of R. Differentially bound regions between two groups were derived by diffbind package of R, and position weight matrices (PWMs) matched with the regions were computed, then their matching TFBSs and TFs were extracted.
Genes that are both differentially expressed and differentially methylated between the two conditions
A pathway analysis result with clusterProfiler package of R (GO database)
A master regulator analysis result computed by VIPER and presented by RedeR. TFs are clustered based on Jaccard Index of their shared target genes.
A master regulator analysis result that shows which TFs are significantly enriched with genes of interest
A comparison of two scores (exclusivity score vs Cosmic enrichment score) of the same elements (hub genes)
I found mis-labeled RNA-Seq samples by comparing 1. variants from RNA-Seq by HaplotypeCaller of GATK, and 2. genotype assays from DNA of the same samples.
A Venn diagram that shows shared target genes of MORF4L1 between a normal (GTEx) and a cancer (TCGA) tissue.
IGV shows aligned reads of two Bam files along with the human genome reference
Pie plots that show how many of the 214 precursor loci are mapped with the Chip-Seq data in each sample.
A gene set enrichment analysis (GSEA) result
A plot that shows where the top 100 specific genes (red) are located among all the genes and stated with the p-value from 1000 permutation test.
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