Sean Davis, github, computational genomics

Sean Davis, NCI, github provides many tutorials using R for comp genomics
https://github.com/seandavi

kayroplot in R,

plot along chromosome in R

https://bernatgel.github.io/karyoploter_tutorial/

structural equations and causal inference

AN INTRODUCTION TO STRUCTURAL EQUATION MODELING FOR ECOLOGY AND EVOLUTIONARY BIOLOGY

http://jarrettbyrnes.info/ubc_sem/

RNAseq coursesource materials

http://www.coursesource.org/courses/teaching-rnaseq-at-undergraduate-institutions-a-tutorial-and-r-package-from-the-genome-0#tabs-0-content=1

Jackson lab genomics Day 1

Moring

install anaconda3 on ubuntu virtualbox

#
hqin@rainboxdash:~/anaconda3/bin/$ ./jupter notebook &


https://thejacksonlaboratory.github.io/bd2k-workshop/ 

samtools view example.bam | less

Linux exercises: up and down arrows, tab for file-names autocomplete

bam file

vcf file (variant call file?)

less test.vcf

mkdir tmpdir
cd tmpdir
cd ..
ls

Essential probability and statistics for introduction to big data

• summary stattistics vs empirical statistics
• Common data transformation, Z-scores
• Bayesian inference
• Multiple hypothesis testing

https://en.wikipedia.org/wiki/Median_absolute_deviation

Bayes's rule

Introductory Data Mining

=====================
Afternoon

curricula:
 all biology are computational
 computational biology are parasite of biology

Approach:
  research project approach using real datasets
  targeted students: professional and academic oriented?

data carpentry's R for genomcis
http://www.datacarpentry.org/R-genomics/


RStudio projects
https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects

args(barplot)
?lm
??lm
help.search("kruskal")

==========
Barke Southern Illinois Medical School, longest-living mouse

===========
Brenton Gravely, RNA genomics

Dscam, over 100 exons, an extreme case of alternative splicing
Schmucker 2000 Cell. Mutually exclusive splicing.
Ig Repeats.  Dimerization are isoform specific.
https://www.ncbi.nlm.nih.gov/pubmed/19934230

Dscam variatiosn between species
Gravely 2005, Cell.

Competing RNA base-pairing is a common mechanism for mutually exclusive splicing in anthropods, Yang 2011 Nature Struc Mol Biol
http://www.nature.com/nsmb/journal/v18/n2/abs/nsmb.1959.html

single cell RNA sequencing
Drosophila S2 cells, each cell show the same splicing isoform.

Drop-seq of Drosophila and human cell to control the number of cells in each droplet.

Oxford nanopore sequencing

1500 RNA binding proteins in human genome

Van Nostrand Nature methods, 2016, eCLIP-seq reveqls RBP-specific binding profiles
http://www.nature.com/nmeth/journal/v13/n6/abs/nmeth.3810.html

*** R learning materials and computational biology

Online courses

Github applied computational genomics
https://github.com/quinlan-lab/applied-computational-genomics

https://github.com/BenLangmead/comp-genomics-class


R programing at Coursera
https://www.coursera.org/learn/r-programming

Data camp https://www.datacamp.com/ 
 introduction, intermediate, and advanced R

Statistics and R
https://www.edx.org/course/statistics-r-harvardx-ph525-1x

http://genomicsclass.github.io/book/pages/classes.html
https://courses.edx.org/courses/HarvardX/PH525.1x/1T2015/info

Quantitative biology workshop
https://www.edx.org/course/quantitative-biology-workshop-mitx-7-qbwx-2

Introduction to Bioconductor: annotation and analysis of genomes and genomics assays
https://www.edx.org/course/introduction-bioconductor-annotation-harvardx-ph525-5x

https://cgondro2.une.edu.au/Rcourse.htm
http://www.springer.com/us/book/9783319144740 . R book, primer to analysis of genomics data using R


Books and articles
An introduction to statistical learning with applications in R
http://www-bcf.usc.edu/~gareth/ISL/index.html

• Stephen J. Eglen's PLOS article. A quick guide to teaching R programming to computational biology students. 
• • 
    

References:
http://hongqinlab.blogspot.com/2013/10/useful-r-materials-for-teaching.html
http://hongqinlab.blogspot.com/2015/06/ngs-tutorials.html

*** computational genomics course plan

data visualization book
https://serialmentor.com/dataviz/

Key topics
Linux
RNAseq
R/Rstudio Rmd

Online:
Regular expression online exercise

RNAseq
biological network


Potential student projects: 
time lapsed image analysis
rDNA reads in yeast genomes ~ lifespan
chemical compounds
network controllability
yeast RLS ~ genomics features
prediction of essential and non-essential genes.
ecology network analysis
aging data comparison
RNN reverse engineering of gene interactions


Reference:
http://hongqinlab.blogspot.com/2015/06/ngs-tutorials.html
http://www-personal.une.edu.au/~cgondro2/Rcourse.htm
Jackson lab workshop
Data Carpentry,
https://github.com/data-lessons/genomics-workshop
https://data-lessons.github.io/genomics-workshop/ 

EdX genomics course