17th 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. Participants are strongly encouraged to bring their own laptops to this year’s Summer Institute. We do not provide computers for attendee use. They are equally strongly encouraged to download and install the software before coming to the Summer Institute.
This is a tentative list and subject to change; please check back here for updates.
Latest update: 06/22/2012 07:01:45 PDT
NOTE:*Items in RED indicate that a newer version of the application is available via the web link than what will be available on the thumb drive.
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.
The thumb drive includes ALL of the packages specified here (AND the additional packages on which they depend) for ALL modules.
| Module 1 | Probability and Statistical Inference: | None |
| Module 2 | Computing for Statistical Genetics: | R 2.15.0 |
| Module 3 | Bayesian Statistics for Genetics: |
R 2.15.0 R coda 0.014-7 |
| Module 4 | Regression and Analysis of Variance: |
Module 4 Data R 2.15.0 R gee 4.13-18 R multcomp 1.2-12 |
| Module 5 | Molecular Genetics and Genomics: | None |
| Module 6 | Population Genetic Data Analysis: |
FStat 2.9.3.2 GDA 1.1 R 2.15.0 R ade4 1.5-0 R adegenet 1.3-4 R ape 3.0-4 R heirfstat 0.04-6 |
| Module 7 | Quantitative Genetics: | None |
| Module 8 | Population Genetics and Association Mapping: |
FBAT 2.0.4 Harpoview 4.2 Module 8 Data R 2.15.0 R HWEBayes 1.3 R GeneticsDesign 1.24.0 |
| Module 9 | Gene Expression Profiling: | None |
| Module 10 | MCMC for Genetics: |
Module 10 Data PHASE 2.1.1 R 2.15.0 Structure 2.3.3 |
| Module 11 | Introduction to QTL Mapping: | QTL Cartographer 2.5.010 |
| Module 12 | Mixed Models in Quantitative Genetics: | None |
| Module 13 | Molecular Phylogenetics: |
BEAST 1.7.2 Mr. Bayes 3.2.1 PHYLIP 3.69 |
| Module 14 | Inference of Relationships and Relatedness: |
BEAGLE 3.3.2 Cervus 3.0.3 COLONY 2.0.2.1 FRANz 1.9.999 MORGAN 3.1 PLINK 1.07 RELPAIR 2.0.1 SNPPIT 1.0 |
| Module 15 | Systems Genetics for Experimental Crosses: |
R 2.15.0 R qtl 1.24-9 R qtlbim 2.0.5 R qtlhot 0.5.2 R qtlnet 1.2.4 |
| Module 16 | Coalescent Theory: |
Lamarc 2.1.8 MCRobot 2.1 Tracer 1.5 |
| Module 17 | High-Dimensional Omics Data: |
|
| Module 18 | Human Quantitative Genetics: |
GCTA 1.0 Merlin 1.1.2 Pedstats 1.0 PLINK 1.07 QTDT 2.6.1 |
| Module 19 | Advanced R Programming for Bioinformatics: | R 2.15.0 |
| Module 20 | GWAS Data Cleaning: |
R 2.15.0 R gdsfmt 0.9.9 R GWASdata 1.0.3 R GWASTools 1.3.6 R SNPRelate 0.9.5 |
| Module 21 | Network and Pathway Analyses of Omics Data: | None |
| Module 22 | Plant and Animal Association Mapping: |
Module 22 Data 1 of 2 Module 22 Data 2 of 2 R 2.15.0 R gplots 2.11.0 R LDheatmap 0.9 R genetics 1.3.6 R multtest 2.12.0 TASSEL 4.0.22 |