OMICs Tutorial
Linux
A beginners guide to the Unix and Linux operating system
Client software (putty/ssh) for Windows users
- Introduction
- Tutorial One
- Listing files and directories
- Making Directories
- Changing to a different Directory
- The directories . and ..
- Pathnames
- More about home directories and pathnames
- Tutorial Two
- Copying Files
- Moving Files
- Removing Files and directories
- Displaying the contents of a file on the screen
- Searching the contents of a file
- link files
- Tutorial Three
- Redirection
- Redirecting the Output
- Redirecting the Input
- Pipes
- Tutorial Four
Power Point download
Aligning sequencing reads to reference genome
An exercise of sequence alignment against reference genome using bowtie2
- Indexing a reference genome
- Introduction
- The bowtie2-build indexer
- Indexing a reference genome
- Extracts summary information from a Bowtie index
- Aligning example reads
- Aligning example reads
- Aligning paired-end reads
- (optional) Use IGV to visualise the alignment results
Power Point download
Metagenomics
An exercise of genome assembly from sequecing reads
- Checking required software
- Quality trimming Illumina paired-end reads
- Assembling reads with Velvet
- Mapping reads back to the assembly
2018-03-12
metagenomics manual
R introduction
An introduction of using R language to conduct data analysis
- Introduction
- Introduction
- R Download and install
- R as a calculator
- Objects in R
- Install packages in R
- Basic R Graphs
- Basic graph functions
- Adding linear model lines on scatter plot
- Adding non-parametric model curves with lowess
- Making scatter plots with smoothed density representation
- Displaying data density on axes
- Using R to do regression analysis
- Basic linear regression
- Logistic regression
- Ploynomial regression
- Ridge regression
- Lasso regression
Power Point download
R advanced application (I am still writing it)
Some advanced application of using R in data science
GLHF
RNA seq A practice of RNA-sequencing data analysis
- Introduction
- Alignment
- Isoform expression and transcriptome assembly
- Differential expression
- Functional annotation of differentially expressed genes
Download the tutorial
WinSCP
Biological network
Part 1
- Visualizing networks using expression data.
- Filtering networks based on expression data.
- Assessing expression data in the context of a biological network.
Download the tutorial
galExpData
galFiltered
Part 2
Download the tutorial
GBM_genelist.txt
GBM_genesample.txt
OVCA_TCGA_MAF.txt
Rapid Verification of Terminators
Download the result
Contact us
Dr. Zhang: jzhang1@hku.hk
Dr. Tong Yin: tongyin9@hku.hk
