jQuery UI

http://msdn.microsoft.com/en-us/magazine/hh127352.aspx

Data Analysis for Genomics

http://genomicsclass.github.io/book/

HarvardX: PH525x Data Analysis for Genomics

Data Analysis for Genomics

The repository of the R markdown files (.Rmd) for the labs shown here is:

http://github.com/genomicsclass/labs

Resources

• Online resources and books
• Finding more help for data analysis

Introduction (week 1)

• Introduction
• Exploratory Data Analysis
• Installing Bioconductor and finding help
• R refresher
• Robust summaries

Microarray and NGS basics (week 2)

• Installing packages from Github
• Reading microarray data
• Downloading data from GEO using GEOquery
• EDA plots for microarray
• Basic Bioconductor infrastructure
• EDA plots for next generation sequencing

Statistical inference and linear modeling (week 3)

• Inference
• Expressing design formula in R
• Linear models
• Basic inference for microarray
• Rank tests
• Monte Carlo methods

Background, modeling and normalization (week 4)

• Background
• Modeling
• Normalization

Distance and prediction (week 5)

• Distance lecture
• Distance and clustering lab
• Dimension reduction and heatmaps
• Prediction lecture
• Cross-validation

Batch effect (week 6)

• Confounding
• SVA, ComBat, PCA and SVD
• Running PCA and SVD in R

Advanced differential expression (week 7)

• Hierarchical modeling and using limma
• Mapping features to genes
• Gene set analysis lecture
• Gene set testing in R
• Multiple testing

Advanced workflows (week 8)

• Visualizing NGS data
• Counting NGS reads in features
• Methylation
• Reading 450K idat files with the minfi package
• Interactive visualization of DNA methylation data analysis
• ChIP-seq
• RNA-seq
• Genome variation

Footnotes for all lectures

• Footnotes

IEEE SPS / UBC ICICS Summer School on Signal Processing and Machine Learning for Big Data

PROGRAM

In natural language processing, latent Dirichlet allocation (LDA) is a generative model that allows sets of observations to be explained by unobserved groups that explain why some parts of the data are similar. For example, if observations are words collected into documents, it posits that each document is a mixture of a small number of topics and that each word's creation is attributable to one of the document's topics. LDA is an example of a topic model and was first presented as a graphical model for topic discovery by David Blei, Andrew Ng, and Michael Jordan in 2003.[1]

https://sites.google.com/site/s3pbigdata2014/program

IEEE SPS / UBC ICICS Summer School on Signal Processing and Machine Learning for Big Data

   

	Tuesday July 29	Wednesday July 30	Thursday July 31	Friday August 1
9:00-9:30	Opening ceremony
9:30-10:30	Konstantinos N. Plataniotis University of Toronto	Angshul Majumdar IIIT-Delhi	Ali Bashashti BC Cancer Agency	Ozgur Yilmaz University of British Columbia
10:30-11:00	Coffee break	Coffee break	Coffee break	Coffee break
11:00-12:00	Vikram Krishnamurthy University of British Columbia	Angshul Majumdar IIIT-Delhi	Tom Levi Plenty Of Fish	Michael Friedlander University of British Columbia
12:00-13:00	Lunch	Lunch	Social event with lunch	Rayan Saab University of California, San Diego
13:00-14:00	Georgios Giannakis University of Minnesota	Martin McKeown University of British Columbia
14:00-14:30	Coffee break	Coffee break
14:30-15:30	Georgios Giannakis University of Minnesota	Li Deng Microsoft Research

Bioinformatics Centre for Computational Medicine (CCM), SickKids, Toronto

Michael Brudno

http://ccm.sickkids.ca/?q=node/32

JQuery UI

http://jqueryui.com/demos/

Java generics

http://docs.oracle.com/javase/tutorial/java/generics/types.html

The most commonly used type parameter names are:

• E - Element (used extensively by the Java Collections Framework)
• K - Key
• N - Number
• T - Type
• V - Value
• S,U,V etc. - 2nd, 3rd, 4th types

public interface Pair<K, V> {
    public K getKey();
    public V getValue();
}

public class OrderedPair<K, V> implements Pair<K, V> {

    private K key;
    private V value;

    public OrderedPair(K key, V value) {
 this.key = key;
 this.value = value;
    }

    public K getKey() { return key; }
    public V getValue() { return value; }
} 

public class Box<T> {

    private T t;          

    public void set(T t) {
        this.t = t;
    }

    public T get() {
        return t;
    }

    public <U extends Number> void inspect(U u){
        System.out.println("T: " + t.getClass().getName());
        System.out.println("U: " + u.getClass().getName());
    }

    public static void main(String[] args) {
        Box<Integer> integerBox = new Box<Integer>();
        integerBox.set(new Integer(10));
        integerBox.inspect("some text"); // error: this is still String!
    }
}

A type variable with multiple bounds is a subtype of all the types listed in the bound. If one of the bounds is a class, it must be specified first. For example:

Class A { /* ... */ }
interface B { /* ... */ }
interface C { /* ... */ }

class D <T extends A & B & C> { /* ... */ }

Tissue specific gene expression

http://www.cureffi.org/2013/07/11/tissue-specific-gene-expression-data-based-on-human-bodymap-2-0/

GTex
Allen Human Brain
Illumina Human Body Map 2.0

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

A draft map of the human proteome

• Min-Sik Kim,
• Sneha M. Pinto,
• Derese Getnet,
• Raja Sekhar Nirujogi,
• Srikanth S. Manda,
• Raghothama Chaerkady,
• Anil K. Madugundu,
• Dhanashree S. Kelkar,
• Ruth Isserlin,
• Shobhit Jain,
• Joji K. Thomas,
• Babylakshmi Muthusamy,
• Pamela Leal-Rojas,
• Praveen Kumar,
• Nandini A. Sahasrabuddhe,
• Lavanya Balakrishnan,
• Jayshree Advani,
• Bijesh George,
• Santosh Renuse,
• Lakshmi Dhevi N. Selvan,
• Arun H. Patil,
• Vishalakshi Nanjappa,
• Aneesha Radhakrishnan,
• Samarjeet Prasad,
• Tejaswini Subbannayya
• et al.

• Affiliations
• Contributions
• Corresponding authors

Nature

 

509,

 

575–581

 

(29 May 2014)

 

doi:10.1038/nature13302

Received

 

09 August 2013 

Accepted

 

31 March 2014 

Published online

 

28 May 2014

Article tools

• Citation
• Reprints
• Rights & permissions
• Article metrics

Abstract

• Abstract• 
• Accession codes• 
• References• 
• Author information• 
• Extended data figures and tables•
• Supplementary information

The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

Subject terms:

• Protein-protein interaction networks
• Protein sequencing
• Proteomic analysis

SSH Tunnelling with Putty (Windows) and Foxy Proxy

SSH Tunnelling with Putty (Windows) and Foxy Proxy

Follow these steps to allow you to view internal web pages.

Open Putty and set:

• host name: myhostname.com
• host port: 22
• Connection > SSH > Tunnels:
  • Pick a source port, say 9870
  • Click Dynamic
  • Click Add
• Click OK to connect. Leave this session open.

Install Foxy Proxy in your web browser and set:

• host or IP address: 127.0.0.1
• port: 9870
• Select SOCKS Proxy
• Select SOCKS v5
• Click Save
• Enable this proxy
• Point your browser to a valid URL

Sublime Text Sublime Text is a sophisticated text editor for code, markup and prose. You'll love the slick user interface, extraordinary features and amazing performance.

Sublime Text
Sublime Text is a sophisticated text editor for code, markup and prose.
You'll love the slick user interface, extraordinary features and amazing performance.


http://www.sublimetext.com/

R Contour / Density Scatter plot

http://stats.stackexchange.com/questions/31726/scatterplot-with-contour-heat-overlay

n = 10000;
a = as.matrix( rnorm(n) );
dim(a) =  c( n/2, 2 );
z = kde2d( a[,1], a[,2], n=50 );
plot( a[,1], a[,2], cex=0.5 );
contour( add=T, z, col=1:11 );

Ubuntu Alt-tab not working

Use 'gnome classic (no effects)'
Restart unity / gnome session with

Ctrl + F2
sudo service lightdm restart

Ubuntu icons gone

I can't find the icons for Terminal, file and folder icons in Nautilus

Fix:
sudo apt-get install gnome-tweak-tool
gnome-tweak-tool
log out and log in using 'gnome-classic' UI