Dates: August 31 – September 2, 2018
Location: ILSB Auditorium
Open Source for Open Science (OSOS) 2018 is a free workshop aimed to familiarize participants with selected open source software and programing tools to be able to conduct quantitative analysis and statistical methods for scientific inquiry. This year we are excited to have six module instructors focusing on an introduction to R, graphics in R, intermediate R tools for data handling, multivariate analysis in R, ecological niche modeling, accessing data repositories, a phylogenetic pipeline tutorial and a WGCNA tutorial. This course is aimed at incoming EEB graduate students; however, you need not be in EEB or a graduate student to attend. In addition, you may receive 1 credit hour of EEBL 612 for this course in the Fall 2018 semester.
Registration form: https://goo.gl/forms/
Danielle Walkup, TAMU
openxlsx
tidyverse
car
PerformanceAnalytics
Pierre Lesne, TAMU
ggplot2
gridExtra
scales
ade4
Adrian Castellanos, TAMU
“Ideally for my modules, each attendee will open up the .R files and attempt to run every install.packages and library function (they are the very first things written). If there are any problems, they should contact me at acastellanos@tamu.edu WITH the error that they are receiving and the operating system they are using.”
Zach Hancock, TAMU
Zach isn’t using R, but everyone needs to download the following programs:
Text editor:
Windows: https://notepad-plus-plus.org
Mac: http://www.barebones.com/
Programs:
Mesquite: https://www.mesquiteproject.
PAUP*: https://paup.phylosolutions.
BEAST2: http://www.beast2.org
TRACER: http://tree.bio.ed.ac.uk/
FigTree: http://tree.bio.ed.ac.uk/
Also, be sure you make an account on the CIPRES portal (https://www.phylo.org).
Please download these programs before the tutorial. The directions for each are relatively straightforward; if you have any difficulties, please let me know at zhancock@bio.tamu.edu or (903) 809-3625.
Pablo Delclos, TAMU
GO.db
impute
preprocessCore
edgeR
WGCNA
flashClust
To make everything easier, the following code below will do it all for you! Just copy and paste into R:
source (“https://bioconductor.
biocLite(“GO.db”)
biocLite(“impute”)
biocLite(“preprocessCore”)
biocLite(“edgeR”)
install.packages(“WGCNA”)
install.packages(“flashClust”)
Rick McMullen, TAMU – PowerPoint file (see below)
Schedule
Friday, August 31
Session 1 – Danielle Walkup
5:00 – 6:30 pm, Intro to R [download files]
Session 2 – Danielle Walkup
6:45 – 8:00 pm, R Intro
Saturday, Sept 1
Session 1 – Pierre Lesne
9:00 – 10:30 am, Graphics in R
Session 2 – Pierre Lesne
10:45 am – 12:15 pm, Multivariate Analysis in R
Session 3 – Adrian Castellanos
2:00 – 3:30 pm, Accessing Data Repositories [download files]
Session 4 – Adrian Castellanos
4:00 – 6:00 pm, Ecological Niche Modeling [download files]
Sunday, Sept 2
Session 1 – Zach Hancock
9:00 – 10:30 am, Rousing the BEAST: A molecular phylogenetic pipeline tutorial [download files]
Session 2 – Pablo Delclos
10:45 am – 12:15 pm, WGCNA tutorial: Incorporating interactions among genes into differential gene expression analysis [download files]
Session 3 – Rick McMullen
1:30 – 3:00 pm, High-Performance Research Computing at TAMU [download file]
Questions may be directed to Jason Martina (jason.marti993@gmail.com) or Anja Schulze (schulzea@tamu.edu).
