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20th Summer Institute in Statistical Genetics: Course Materials & Software

SISG Course Materials and Software

The following list links to the handouts and publicly available software (if any) used by each module for SISG 2015.

some modules will require participants to bring a laptop and will use it in all sessions. Additionally, participants are STRONGLY encouraged to download and install the software BEFORE coming to the Institute. Participants will have free online access while they are on the University of Washington campus.

This is a tentative list and subject to change; please check back here for updates.

Latest update: 07/30/2015 15:14:20 PDT

NOTE:**With regards to R package downloads, we have only listed those R packages specifically requested by the instructor. Additional packages required for successful installation of the specified packages are *not* explicitly listed here, as R normally resolves dependencies and downloads required packages automatically.

Module # Module Name

Module Handouts

Module Software

Module Video
Module 1 Probability and Statistical Inference:

Handout No Software 1.04.a
1.07.a
1.08.a
1.09.a
1.10.a
Module 2 Molecular Genetics and Genomics: Handout No Software 2.05.a
2.06.a
2.07.c
2.08.b
2.09.a
2.10.a
Module 3 Introduction to R: Handout

R 3.2.0 3.01.a
3.01.b
3.02.a
3.02.b
3.03.a
3.03.b
3.04.a
3.04.b
3.05.a
3.05.b
3.06.a
3.06.b
3.07.a
3.07.b
3.08.a
3.08.b
3.08.c
3.09.a
3.09.b
3.10.a
Module 4 Accessing Biomedical Big Data: Resources Git Mac
Git Windows
GitHub Windows
GitHub Mac
Setup Walk Thru Git/GitHub
GitHub Windows Config
R
r package affy
r package data::table
r package dplyr
r package ggplot2
r package GEOmetadb
r package GEOquery
r package ggthemr
r package ImmuneSpaceR
r package knitr
r package limma
r package reshape2
r package rfigshare
r package SRAdb
RStudio
Rtools
4/1.01.a
4/1.01.b
4/1.02.a
4/1.03.a
4/1.04.a
4/1.05.a
4/1.06.a
4/1.07.a
4/1.08.a
4/1.09.a
4/1.10.a

Module 5 Regression and Analysis of Variance: Handout

Module 5 Data and Notes
R 3.2.0
R package gee
R package multcomp
RStudio
5.01.b
5.02.b
5.02.c
5.03.a
5.04.a
5.05.a
5.06.a
5.07.a
5.09.a
5.10.a
Module 6 Gene Expression Profiling: Handout

Module 6 Data and Notes
TBA
6.01.a
6.02.a
6.04.b
6.05.a
6.06.b
6.06.c
6.07.a
6.08.a
6.09.a
6.10.b
Module 7 Elements of R for Genetics and Bioinformatics: Handout

TBA TBA
Module 8 Visualization of Biomedical Big Data: Resources Git Mac
Git Windows
GitHub Windows
GitHub Mac
Setup Walk Thru Git/GitHub
GitHub Windows Config
RStudio
Rtools

8/2.01.a
8/2.02.a
8/2.03.a
8/2.03.b
8/2.04.a
8/2.05.a
8/2.05.b
8/2.06.a
8/2.07.a
8/2.08.a
8/2.08.b
8/2.09.a
8/2.10.a
Module 9 Population Genetic Data Analysis: Handout

R 3.2.0
R package adegenet
R package ape
R package hierfstat
RStudio

TBA
Module 10 Quantitative Genetics: Handout

TBA TBA
Module 11 Genetic Epidemiology: Handout

No Software TBA
Module 12 Supervised Methods for Statistical Machine Learning: Resources
R
r package akima
r package boot
r package car
r package class
r package e1071
r package gam
r package gbm
r package glmnet
r package ISLR
r package leaps
r package MASS
r package pls
r package randomForest
r package ROCR
r package tree
12/3.01.a
12/3.02.a
12/3.03.a
12/3.04.a
12/3.05.a
12/3.06.b
12/3.07.a
12/3.08.a
12/3.09.a
12/3.10.a
Module 13 Association Mapping: GWAS and Sequencing Data: Handout

R 3.2.0
PLINK
TBA
Module 14 QTL Mapping: Handout

Windows QTL Cartographer V2.5_011

TBA
Module 15 Mixed Models in Quantitative Genetics: Handout

TBA TBA
Module 16 Unsupervised Methods for Statistical Machine Learning: Resources R
r package fastICA
r package glasso
r package igraph
r package ISLR
r package NMF
r package PMA
r package samr
16/4.01.a
16/4.02.a
TBA-16/4.03.a
16/4.04.a
16/4.05.a
16/4.06.a
16/4.07.a
16/4.08.a
16/4.09.a
16/4.10.a
Module 17 Advanced R Programming for Bioinformatics: Handout

TBA TBA
Module 18 MCMC for Genetics: TBA

PHASE
R 3.2.0
Structure
TBA
Module 19 Statistical & Quantitative Genetics of Disease: TBA

R 3.2.0
RStudio
TBA
Module 20 Reproducible Research for Biomedical Big Data: Resources Git Mac
Git Windows
GitHub Windows
GitHub Mac
Setup Walk Thru Git/GitHub
GitHub Windows Config
R
r package devtools
r package dplyr
r package ggplot2
r package knitr
r package knitrBootstrap
r package lubridate
r package packrat
r package plyr
r package rmarkdown
r package roxygen2
RStudio
Rtools
20/5.01.a
20/5.02.a
20/5.03.a
20/5.04.a
20/5.05.a
20/5.06.a
20/5.07.a
20/5.08.a
20/5.09.a
20/5.10.a
Module 22 Bayesian Statistics for Genetics: TBA

Module 22 Data
R 3.2.0
R package dplyr
R package ggplot2
R package coda
None Available
Module 23 Advanced Quantitative Genetics: TBA

TBA TBA
Module 24 Pathway & Network Analysis for Omics Data: TBA

No Software TBA
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