Djoser Genomics

@djosergenomics.github.io

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Exploring #SyntheticBiology & #Bioinformatics + Documenting my learning journey | Built by @noureldenrihan.bsky.social | 🌐 djosergenomics.github.io

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A Schematic Showing a Brief Overview of the Proposed Pipeline
PyMOL Visualization of Structures of Tyrosinase Enzyme (Red Alpha Helices, Yellow Beta Sheets, Green In between Loops) (PDB ID: 3NM8)
Djoser Genomics Step Pyramid Drawn by Opentrons virtual robot
Scroll 8 of Bulk RNAseq Tutorial Codex: Djoser's Discoveries
Scroll 7 of Bulk RNAseq Tutorial Codex: Thutmose's Trends
Scroll 6 of Bulk RNAseq Tutorial Codex: Ramses' Plots
Scroll 5 of Bulk RNAseq Tutorial Codex: Menkaure's Measures
Scroll 4 of Bulk RNAseq Tutorial Codex: Khafre’s Connections
Scroll 3 of the Bulk RNA-seq Tutorial Codex: Khufu's Calculations
Scroll 2 of Djoser’s Bulk RNAseq Tutorial Codex: Hesy-Ra's Diagnostics
Scroll 1 of Djoser’s Bulk RNAseq Tutorial Codex: Imhotep's Insights
Enrichment Plot showing upregulation of the most significant GSEA pathway which is KEGG Allograft Rejection
Dotplot showing Top 10 KEGG Pathways
Dotplot showing Top GO Enrichment terms (BP,MF,CC)
Sample to Sample distance heatmap, HS02 & CD01 are the most different, HS02 & HS03 cluster together, suggesting shared expression, CD03 appears distinct from other CD samples, possibly due to biological or technical factors.
Expression distributions across samples show stable medians with no major batch effects, HS02 & HS03 has a slight outlier, CD03 follows expected trends.
The MA plot highlights significantly differentially expressed genes (p < 0.05) between disease & healthy samples, Most genes stay around log2FC = 0, while some show strong up/downregulation.
Heatmap of all 771 DEGs shows HS & CD samples clustering separately, revealing distinct expression patterns.
Volcano plot of disease vs. healthy, It shows differentially expressed genes with log2FC > 1 or < -1 & padj < 0.05 are in red.
PCA plot with sample labels, PC1 vs PC2, PC1 shows 39.2% variance & PC2 shows 26.7% variance
Sample to Sample distance heatmap, CD01 and CD02 are highly similar, while HS02 and CD03 are the most different. HS01 and HS02 cluster together, suggesting shared expression. CD03 appears distinct from other CD samples, possibly due to biological or technical factors.
Expression distributions across samples show stable medians with no major batch effects, HS02 has a slight outlier, CD01 follows expected trends.
The MA plot highlights significantly differentially expressed genes (p < 0.05) between disease & healthy samples, Most genes stay around log2FC = 0, while some show strong up/downregulation.
Heatmap of my 645 DEGs shows HS & CD samples clustering separately, revealing distinct expression patterns.
Volcano plot of disease vs. healthy, It shows differentially expressed genes with log2FC > 1 or < -1 & padj < 0.05 are in red.
PCA plot with sample labels, PC1 vs PC2, PC1 shows 39.9% variance & PC2 shows 26.4% variance
Go Enrichment Analysis of how melatonin alleviates TNF-α-induced damage in human coronary artery endothelial cells (HCAECs) using RNA-seq
Old DESeq2 P-value Histogram showing U shapped appearance
Dispersion Estimates Plot
PCA Plot showing PC1: 96% variance and PC2: 1% variance
Top 10 Over-represented Categories in Wallenius Method - Goseq Plots
DESeq2 MA Plot
DESeq2 Dispersion Estimates
DESeq2 P-Value Histogram
DESeq2 PCA Plot