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Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output

License: GNU General Public License v3.0

Shell 20.96% R 79.04%

16s-demo's Introduction

Hi there 👋

Welcome to my GitHub profile!

R Packages

scRUtils: Single-Cell Sequencing Analysis Utilities [Vignette]

NGS Tutorials

RNA-Seq: RNA-seq Data Analysis
- Differential gene expression (DGE) analysis
- Differential transcript expression (DTE) analysis
- Differential transcript usage (DTU) analysis
Microbiome: 16S rDNA V3-V4 amplicon sequencing analysis
Tertiary analysis
- GO enrichment analysis with topGO, clusterProfiler & Enrichr/enrichR
- Visualize enrichment of genomic signals on targets or regions using EnrichedHeatmap

Misc.

Create a GitHub Pages site for your repository
Create stacked violin plots from Seurat, SingleCellExperiment and data.frame objects
Gallery showcasing Pandoc syntax highlight styles before and after version 2.11
Short examples of using R in data analysis and visualisation
- National survey
  - Deaths registered monthly in England and Wales
  - COVID-19 Vaccination Statistics in England
- Gene expression
  - Visualise differential expression analysis results with MA plot
  - Normalisation of bulk RNA-seq counts
  - Plot ligand-receptor expression on UMAP and t-SNE projection
- Others
  - Visualise interaction between 2 variables with parallel sets diagrams
  - Testing of the Spatial Image Analysis of Tissues (SPIAT) R package

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