These are course materials based on R. This course was offered in Spring of 2010, 2011, 2012. Later materials are in Spel.eLearn site and http://sunrays.spelman.edu/hqin/

425 visits.

These are course materials based on R. This course was offered in Spring of 2010 and 2011.

• Final quiz is here. Good luck.

• Final written reports are due on May 4, 5pm. This report should be written in the style of a scientific publication. In addition to your reports, R codes and running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.

• Final take home quiz will be posted on April 28th. Your R codes, discussion of results and conclusions should be emailed to the instructor by May 3rd, 5pm. Discussion of the results and conclusions should be written in WORD document. This is an independent test. No collaboration is allowed. Late submission will not be accepted.

• Final written reports are due on May 1, 5pm. This report should be written in the style of a scientific publication. In addition to your reports, R codes and running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.

• Final written reports are due on April 27, 5pm. This report should be written in the style of a scientific publication. In addition to your reports, R codes and running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.

• Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication. In addition to your reports, R codes and running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.

• Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication. In addition to your reports, codes, running results, and necessary supporting materials should all be electronically submitted to the instructor. Please see your syllabus for detailed requirement.

• Oral presentation is on April 27 in class. Rubric will be provided.

• Final take home quiz will be posted on April 30th. Your R codes, discussion of results and conclusions should be emailed to the instructor by May 3rd, 5pm. Discussion of the results and conclusions should be written in WORD document. This is an independent test. No collaboration is allowed. Late submission will not be accepted.

• Final take home quiz will be posted on April 30th. Your R codes, discussion of results and conclusions should be emailed to the instructor by May 3rd, 5pm. Discussion of the results and conclusions should be written in WORD document This is an independent test. No collaboration is allowed. Late submission will not be accepted.

• Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication.

• Oral presentation is on April 27 in class.

Final take home quiz will be posted on April 30th. Your R codes, discussion of results and conclusions should be emailed to the instructor by May 3rd, 5pm. Discussion of the results and conclusions should be written in WORD document This is an independent test. No collaboration is allowed. Late submission will not be accepted.

Final written reports are due on April 27, 5pm. Late reports will not be accepted. This report should be written in the style of a scientific publication.

Oral presentation is on April 27 in class.

;

Old contents

• Input, ouput, plots, packages; homework1
• Quiz1 (functions, loops, input, output)
• Computational thinking and p-value; t-test and p-value
• distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;
• Libya HIV case;
• Microarry, clustering analysis, Prostate cancer case;
• Protein structure and protein networks
• Modeling of aging and genetic changes;
• QUIZ 2;
• Regression, Peanut genotypes and phenotypes association;
• Probability and likelihood estimation

• Keys to #3,#4 in Quiz2

Abstract submission for Research Day is due on March 15, Monday.

  Abstract submission for Research Day is due on March 15, Monday. 

All groups should email their draft research abstract to the instructor by the end of March 5

• Quiz 2. Your answers should be emailed to the instructor by 12:00pm on Feb 23, Tuesday, 2010.

• Quiz 2 on Feb 23, Tuesday.

• Quiz 2 on Feb 23, Tuesday

• Computational thinking, simulation and p-value

• Assignment 1, due Tuesday Feb 9, 2010

• Assignment 2, continued

• KaKs, growth fitness, protein connectivity in yeast PIN
• Assignment 2

• Permutation to calculate the p-value of Ka difference in interacting protein pairs

1. Assignment 2, continued

• Computational thinking, permutation and p-value
• Permutation to calculate the p-value of Ka difference in interacting protein pairs

Assignment 2, continued

• Computational thinking, permutation and p-value Assignment 2, continued

• Computational thinking, permutation and p-value Assignment 2, continued

• Computational thinking, permutation and p-value Assignment 2, continued

• Computational thinking, permutation and p-value Assignment 2, continued

• Computational thinking, permutation and p-value Assignment 2, continued

Hong Qin, Spring 2010, Spelman

Hong Qin

• KaKs, growth fitness, protein connectivity in yeast PIN Assignment 2

• KaKs, growth fitness analysis, protein connectivity in yeast PIN Assignment 2

• KaKs, growth fitness analysis, protein connectivity in yeast PIN

Lectures and labs

• An overview of R;

• Basic programming in R;
• Quiz 1
• Input, output, plots, packages;
• Assignment 1

• Meeting at GaTech, March 26-28, 2010

• Input, output, plots, packages;

• Assignment 1

• Input, output, plots, packages;

• Quiz 1

 script for salary example; 

• Spelman Research Day, April 16, 2010

Announcements

• Meeting at GaTech, March 26-28, 2010
• Spelman Research Day, April 16, 2010

• Basic programming in R;

Software tools

• R for windows
• Notepad++

Old contents

1. R reference card,1
2. R reference card,2

1. R reference card,1
2. R reference card,2

• An overview of R;

• Basic programming in R;

• Input, ouput, plots, packages; homework1
• Quiz1 (functions, loops, input, output)
• Computational thinking and p-value; t-test and p-value
• distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;
• Libya HIV case;
• Microarry, clustering analysis, Prostate cancer case;
• Protein structure and protein networks
• Modeling of aging and genetic changes;
• QUIZ 2;
• Regression, Peanut genotypes and phenotypes association;
• Probability and likelihood estimation;

1. An overview of R; Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.

1. An overview of R

\\ Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.

1. An overview of R\\ Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.

1. An overview of R Reading assignment: Fraser et al 2002, Science, Evolutionary rate in the protein interaction network.

1. essential genes and connectivity
2. Gasch expression

1. An overview of R

1. Documents at CRAN

1. Computer basics

1. Beginner R by Mathews;

\\

9am-11:30am, Tue & Thur, Sci 246

Computing in Genomics and Proteomics

Spring 2010, Spelman

Computing in Genomics and Proteomics, Spring 2010, Spelman

1. R reference card
2. An Introduction to R, pdf

1. Essential Bioinformatics, by J Xiong

2. First course in statistical programming using R, by WJ Braun & DJ Murdoch

1. Begginer R by Mathews;
2. R for Bioinformatics by Krijnen;

1. Essential Bioinformatics
2. First course in statistical programming using R

Reading materials:

1. R reference card
2. An Introduction to R, pdf
3. Contributed docs on R at CRAN

Reference materials:

Please install the following software on your computers

Please install the following software on your computers

• Notepad++
• R for windows

1. Protein structure and protein networks

1. Computer basics

Computing in Genomics and Proteomics, Spring 2010

Lectures and labs

1. [[http://www.bioinformatics.org/ctls/download/biol595/computer.basics.ppt | Computer

basics]]

1. An overview of R
2. Basic programming in R;
3. Input, ouput, plots, packages; homework1
4. Quiz1 (functions, loops, input, output)
5. Computational thinking and p-value; t-test and p-value
6. distance between sequences, distance matrix and phylogeny; 2003 SARS outbreak; riddle of the giant panda;
7. Libya HIV case;
8. Microarry, clustering analysis, Prostate cancer case;
9. Protein structure and protein networks, (Graduating seniors should write a one-page summary on the paper, Kim, et al, 2006, Science. "Relating 3-dimentioal structures to protein networks provides evolutionary insights". Your summary should explain the key findings and methods used, point out a few weakness. )
10. Modeling of aging and genetic changes;
11. QUIZ 2;
12. Regression, Peanut genotypes and phenotypes association;
13. Probability and likelihood estimation;

Reading materials:

1. R reference card
2. An Introduction to R, pdf
3. Contributed docs on R at CRAN
4. R, UW
5. R online tutorial, ISU
6. R online tutorial, Mercury
7. Programming in R, UC Riverside

Software tools

1. R (Windows) installation

Papers

1. Libya HIV
2. Kelly 2008 Light drinking in pregnancy, a risk forbehavioural problems and cognitive deficits at 3 years of age?

3. Siege of Athens
4. yeast tiling array
5. yeast LOH and life span
6. Human metabolic profile variation

Related sites:

• http://ocw.mit.edu/ans7870/6/6.891/f04/labs/lab1.html
• http://ocw.mit.edu/ans7870/6/6.891/f04/labs/laboratory2.htm
• http://www.sys-bio.org/sbwWiki/sysbiolabmembers/498_systems_and_synthetic_biology_spring_2008
• http://www.sys-bio.org/index.htm
• http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-895Fall-2005/LectureNotes/index.htm
• Number Count