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18th Summer Institute in Statistical Genetics: Computing & Software

SISG Software

The following list links to the publicly available software (if any) used by each module. There will not be a SISG Computer Laboratory NOR will there be a thumb drive available with module software as provided in past years. Participants are STRONGLY encouraged to bring their own laptops to this year's Institute. 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: 06/13/2013 08:30:20 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 1 Probability and Statistical Inference: None
Module 2 Molecular Genetics and Genomics: None
Module 3 Introduction to R: R 3.0.1
Module 4 Bayesian Statistics for Genetics: R 3.0.1
R coda
Module 5 Regression and Analysis of Variance: Module 5 Data
R 3.0.1
R gee
R multcomp
Module 6 Population Genetic Data Analysis: R 3.0.1
Module 7 Quantitative Genetics: BLUPF90
Module 7 Data
TM and GS3
Module 8 Population Genetics and Association Mapping: Haploview
LocusZoom
PLINK
R 3.0.1
R HWEBayes
R GeneticsBase
R GeneticsDesign
Module 9 Gene Expression Profiling: BEDtools
bowtie2
Module 9 Data
R 3.0.1
R edgeR
SAMtools
Module 10 MCMC for Genetics: Module 10 Data
PHASE
R 3.0.1
Structure
Module 11 Introduction to QTL Mapping: QTLCartographer
Module 12 Mixed Models in Quantitative Genetics: BLUPF90
Module 12 Data
TM and GS3
Module 13 Molecular Phylogenetics: Beast
Java
MrBayes
Phylip
Module 14 Elements of R for Genetics and Bioinformatics: R 3.0.1
Module 15 Coalescent Theory: Lamarc
MCRobot (Windows Only)
R 3.0.1
Tracer

Module 16 High-Dimensional Omics Data: R 3.0.1
R akima
R boot
R class
R e1071
R gam
R gbm
R glmnet
R ISLR
R leaps
R MASS
R pls
R randomForest
R ROCR
R tree
Module 17 Human Complex Traits: GCTA
PedStats
Merlin
QTDT
PLINK
Module 18 Advanced R Programming for Bioinformatics: R 3.0.1
Module 19 Network and Pathway Analyses of Omics Data: GSEA/MSigDB
R 3.0.1
R GSA
R WGCNA
Module 20 Animal Genetic Data Analysis: 7-zip
Beagle 3.3.2
Haploview
R 3.0.1

Module 21 Statistical Genetics for Forensic Science: None
Module 22 Beginning Scripting for Biologists: PuTTY (Windows Only)
Python 2.7
Xming (Windows Only)
XQuartz (Mac Only)