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Name: I-Hsuan Lin

Type: User

Company: University of Manchester

Bio: Bioinformatician

Location: United Kingdom

Blog: https://sites.google.com/site/ihsuansite

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

I-Hsuan Lin's Projects

16s-demo

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

16s-rdna-v3-v4

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

augur

Cell type prioritization in single-cell data

biomformat

Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html

bsgenome.bdistachyon.jgi.bd3.1

Full genome sequences for Brachypodium distachyon (JGI version 3.0 assembly)

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

compare-pandoc-styles

The Pandoc syntax highlighting changed in version 2.11 when showing R Markdown. The gallery shows comparisons before and after version 2.11.

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

deseq2

Differential expression of RNA-seq data using the Negative Binomial

enrichedheatmap-demo

Quick guide to visualize enrichment of genomic signals on targets or regions using EnrichedHeatmap

go-enrichment-analysis-demo

Working Demo on GO Enrichment Analysis using topGO, clusterProfiler and Enrichr/enrichR. Visit repo website for HTML output

grcbook_ch14

Supplemental codes for the Chapter 14 Chromatin Sequencing and Data Analysis of the NYMU-GRC eBook 基因體技術與資料分析手冊

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

methylationworkshop2014

Collection of shell & R scripts used in the 2014 Methylation Analysis Workshop

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page: