Categories

• bioinformatics 30
• research 20
• RNA-seq 2
• microarray 1
• DESeq2 1
• teaching 1
• maps 3
• gpx 1
• genome 6
• text_analysis 4
• machine_learning 10
• blogging 1
• animation 1
• r_vs_python 1
• shiny 3
• ggplot2 1
• writting 1
• Genetics 2
• flexdashboard 3

bioinformatics

• How to generate dbSNP153(hg19) from dbSNP153(hg38,GRCH38)
• Next generation protocol to bcftools in medical genetics research
• How to prepare a computational biology work station in MCRI
• How to apply deeptools for Medip-seq and MBD-seq analysis
• Genome-wide multiple bedgraph data analysis with Intervene
• How to update hapmap2 and hapmap3 from hg18 to hg19 or hg38
• Genetics and epigenetics of pancreatic and cholangiocarcinoma
• Genetic and epigenetic of esophageal squamous cell carcinoma
• Advances in Genetic and epigenetic of Hepatocellular Carcinoma
• How to apply R to prepare fancy figures in the manuscript
• Most Important Database for Human Biomedical Research
• How to get genomic coordinates for all protein domains
• How to Understand Human Cancer
• How to Submit NGS Seqeuencing data to SRA
• Resources for flow cytometry bioinformatics analysis
• How to use plink1.9/plink2 to do human genetics research
• RNA-seq data to reveal novel response mechanism to bacterial
• RNA-seq data with metaphlan2 to reveal novel response mechanism to bacterial
• EAS and SAS data in GenomeAsia100K panel
• Genomics, Genomics and Related Disciplines
• How to reformat GeneSky GSA report to Plink
• How to merge 7000 VCF files with bcftools merge?
• Automatic GWAS and Post-GWAS Analysis Pipeline
• How to install ANNOVAR in DeepThought@UW-Madison
• How to Prepare Annotation DB Folder for Bioinformatics Analysis
• How to Prepare China and USA Map with R
• FDA and drug development pipeline
• How to Install Ensembl Variant Effect Predictor
• FDA approved drugs and the mechanism
• Bioinformatics Skills Required

research

• Novel 2019 coronavirus genome in Wuhan, China and USA
• Robust Region-Based Rare-Variant Test to UKBB-Seq Data
• Genome-wide DNA methylation to human atrial fibrillation
• Genome-wide bisulfite sequencing to human tissue samples
• Epigenome Research to Human Cancers with WGBS
• Genomics, Environment Interaction, Epigenetics and Aging
• Population Genetics in East Asian and Allele Frequency
• Genetic and Epigenetic based Intra-Tumor Heterogeneity
• Electronic health/medical records (EHR/EMR) data analysis
• US-FDA Artificial Intelligence and Machine Learning Discussion
• Artificial intelligence in risk prediction and diseases diagnosis
• How to design and conduct a biomedical research in MCRI
• Gene ID Transfer with R between Symbol, Gene ID and KEGG ID
• Human Population Genetics and related data operation
• How to set up github and use it to accelerate your research
• Environment Setting in All My Previous Working Station
• How to Install HTseq in Linux and STAR for RNA-seq
• How to apply MACS2 to identify methylation peaks with MBD-seq
• DNA methylation and Epigenetic research in Human Population
• Multi-Omics of Characterization of the Cancer Cell Line Encyclopedia

RNA-seq

• DESeq2 Course Work
• exprAnalysis package

microarray

• exprAnalysis package

DESeq2

• DESeq2 Course Work

teaching

• DESeq2 Course Work

maps

• How to apply R for Plotting 3D maps and location tracks
• How to map your Google location history with R
• USA/ Canada Roadtrip 2016

gpx

• USA/ Canada Roadtrip 2016

genome

• Gene homology Part 3 - Visualizing Gene Ontology of Conserved Genes
• How to build a Shiny app for disease- & trait-associated locations of the human genome
• Gene homology Part 2 - creating directed networks with igraph
• Creating a network of human gene homology with R and D3
• Exploring the human genome (Part 2) - Transcripts
• Exploring the human genome - Gene Annotations

text_analysis

• Characterizing population with principle componment analysis
• Analysing the Gilmore Girls' coffee addiction with R
• Creating a Gilmore Girls character network with R
• Is 'Yeah' Josh and Chuck's favorite word?

machine_learning

• Explaining complex machine learning models with LIME
• Dealing with unbalanced data in machine learning
• Building meaningful machine learning models for disease prediction
• Plotting trees from Random Forest models with ggraph
• Hyper-parameter Tuning with Grid Search for Deep Learning
• Building deep neural nets with h2o and rsparkling that predict arrhythmia of the heart
• Predicting food preferences with sparklyr (machine learning)
• Feature Selection in Machine Learning (Breast Cancer Datasets)
• Extreme Gradient Boosting and Preprocessing in Machine Learning - Addendum to predicting flu outcome with R
• Can we predict flu deaths with Machine Learning and R?

blogging

• How to set up your own R blog with Github pages and Jekyll Bootstrap

animation

• Animating Plots of Beer Ingredients and Sin Taxes over Time

r_vs_python

• R vs Python - a One-on-One Comparison

shiny

• Scratching the Surface of Gender Biases
• New features in World Gender Statistics app
• Exploring World Gender Statistics with Shiny

ggplot2

• Conditional ggplot2 geoms in functions (QTL plots)

writting

• Science Writing: Guidelines And Guidance in Medical Research

Genetics

• Data Science in Population Genetics and Medical Genetics
• Geneics and epigeneitcs of rheumatoid arthritis and osteoarthritis

flexdashboard

• Genome-wide cell-free DNA fragmentation in patients with cancer
• (5R)-5-Hydroxytriptolide and Epigenetics of Rheumatoid Arthritis
• Recessive Diplotype Identify Novel Hemochromatosis Gene