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`Computational Statistics,Genetics & Microbiology.`
======================================================

`Susan Holmes <http://www-stat.stanford.edu/~susan/>`_,

.. Statistics, Stanford, Sequoia Hall, CA 94305.

*******************
Schedule & Location
*******************

MW 11:00-12:15, McCullough  122.
Labs F 11-12, GAtes B12.

****************
Instructor & TAs
****************

Instructor
----------

`Susan Holmes <http://www-stat.stanford.edu/~susan>`_

  * Office: Sequoia Hall #102
  * Phone: 725-1925, 
  * Email: susan  AT stat DOT stanford etc
  * Office hours: M, F 2:15-3:15 

Teaching Assistant
------------------
Austen Head

* Office: Sequoia Hall 208
* Office hours: Thursday 2.30-3.30
* `Email <https://stanfordwho.stanford.edu/auth/lookup?search=Austen%20Head>`_

.. Forum:


This course will show a series of statistical concepts in action.
We will cover a series of case studies showing you how to use R and 
relevant tools to analyse your complex biological data sets.

*****************
Computer examples
*****************

We will be using `R <http://cran.r-project.org>`_ for most examples,
and more precisely the `Bioconductor <http://www.bioconductor.org/>`_
suite. 
Both of these sites have large numbers of documents and tutorials.

*************
Prerequisites
*************

Some familiarity with linear algebra and statistical methods.


**********
Evaluation
**********
* Class participation and scribing; 20%
* Labs/homework (5 total, best 4 count); 40%
* midterm (project proposal); 15%
* final project (according to Stanford calendar: due on June, 13th); 25%


Preliminary Schedule
--------------------
  `Results of survey <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/resultsquest.pdf>`_

.. csv-table:: 
   :header: "Week", "Subject", "Lect Link","Lect Link", "Lab Friday"

   April 2-6,  Genomes and Sequences, `Lect 1 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/ohintro.pdf>`_ , `Lect2 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/ohgenetics.pdf>`_, `Lab 1 <./exs/lab1.html>`_
   April 9-13, CpG Islands Multinomials/Markov Chains/HMMs , `Lect3 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/ohhmm1.pdf>`_ , `Lect4 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/ohhmm2.pdf>`_ , `Lab 2 <./exs/lab2.html>`_   
   April 16-20, Multivariate Examples , `Lect 5 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect5JoeyGGplot.pdf>`_ , `Lect 6 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect6-multiv.pdf>`_, `Lab 3 <./exs/lab3.html>`_
   April 23-27, PCA-MDS-CA and graphs , `Lect 7 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect7-MDSCA.pdf>`_, `Lect 8 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect8-PresAbs.pdf>`_, `Lab 4 <./exs/lab4.html>`_
   April 30-May 4, ML and Bayesian estimation(MCMC)  , `Lect 9 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect9-BayesGibbs.pdf>`_ , `Lect 10 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect10-MCMCGibbs.pdf>`_ , None
   May 7-11,  Phylogenetic Trees/ Bootstrap, `Lect 11 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/mcmurdie_clust_trees_v08.pdf>`_, `Lect 12 <https://coursework.stanford.edu/access/content/group/Sp12-BIOMEDIN-366-01_Sp12-STATS-366-01/Lect12-BootPhylo.pdf>`_, `Lab 5 <./exs/lab5.html>`_
   May 14-18, Microarray Normalization/lowess, `Lect 13 <./microarray.html>`_ , Lect 14, None
   May 21-25, Multivariate Analyses plots/interpretation/permutation tests, Lect 15, Lect16, None
   May 28-June 1, Kernel Methods , Lect 17, Lect18, None 
   June 4-8, High Throughput sequence analyses , Lect 19, Lect20, None

*****************
Materials
*****************

.. toctree::
   :maxdepth: 1

   exs/CrashCourseBiology.rst
   exs/Chargaff.rst
   exs/stringdata.rst
   exs/Markov1.rst
   hmmR2.rst
   exs/HMM1.rst
   exs/algos.rst
   pca.rst
   svdmds.rst
   tables.rst
   Mixt.rst
   Gibbs.rst
   microarray.rst


..   exs/cpgislands
    
Assignments
----------------

.. toctree::
   :maxdepth: 1

   exs/hw1.rst
   exs/lab1.rst
   exs/lab2.rst
   exs/lab3.rst
   exs/lab4.rst
   exs/lab5.rst

   
Lecture Materials
---------------------

   For relevant slides click on time table above which will lead you to the coursework
   repository.

Acknowledgements
----------------

I was inspired to rewrite my previous notes for this course up as a sphinx document by the wonderful work of `Avril Coghlan <http://www.ucc.ie/microbio/avrilcoghlan/>`_ and her little book on Bioinformatics.

Jonathan Taylor helped me through the process of getting started using sphinx, especially interfacing it with ``R``.

All the cartoons from the website are shamelessly poached from `Randall Munroe s xkcd <http://xkcd.com>`_ webcomics.

License
-------
The content of this website are licensed under a `Creative Commons Attribution Share Alike 3.0 License
<http://creativecommons.org/licenses/by-sa/3.0/>`_.  |imagecc|


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.. |xkcd|   image:: ./_static/logo.png
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