Bundle:

CGR (Windows version)

Version:

1.0-5

Date:

2006-5-22

Title:

Classic Genetics in R

Author:

Jing hua Zhao in collaboration with other colleagues

Maintainer:

Jing hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

BundleDescription:

This is an experimental package bundle based on the R packages pathmix and pointer.

License:

Programs included in this package by Jing hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors.

URL:

http://www.mrc-epid.cam.ac.uk/~jinghua.zhao

Name:

R/gap (Windows version)

Version:

1,1-3

Date:

2011-6-6

Author:

Jing hua Zhao in collaboration with other colleagues, and with help from Kurt Hornik and Brian Ripley of the R core development team

Maintainer:

Jing hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

Description:

It is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

License:

Programs included in this package by Jing hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors.

URL:

http://www.mrc-epid.cam.ac.uk/~jinghua.zhao

Reference Manual (PDF)

Vignette (PDF)

Name:

kinship (Windows version)

Version:

1.1.1

Date:

2011-6-6

Title:

mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees

Author:

Beth Atkinson (atkinson@mayo.edu) for pedigree functions. Terry Therneau (therneau@mayo.edu) for all other functions.

Maintainer:

Jing hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

Depends:

survival, nlme, lattice

Description:

coxme: general mixed-effects Cox models; kinship: routines to create and manipulate n by n matrices that describe the genetic relationships between n persons; pedigree: create and plot pedigrees; bdsmatrix: a class of objects for sparse block-diagonal matrices (which is how kinship matrices are stored); gchol: generalized cholesky decompositions.

License:

GPL (>=2)

URL:

http://www.mayo.edu/biostatistics

Reference Manual (PDF)

Vignette (PDF)

Name:

lmm (Windows version)

Version:

0.3-5

Date:

2008-8-26

Title:

Linear mixed models

Author:

Original by Joseph L. Schafer <jls@stat.psu.edu>.

Maintainer:

Jing hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

Description:

Some improved procedures for linear mixed models

License:

The software may be distributed free of charge and used by anyone if credit is given. It has been tested fairly well, but it comes with no guarantees and the authors assume no liability for its use or misuse.

URL:

http://www.stat.psu.edu/~jls/index.html

Reference Manual (PDF)

Name:

pan (Windows version)

Version:

0.3

Date:

2011-4-28

Title:

Multiple imputation for multivariate panel or clustered data

Author:

Original by Joseph L. Schafer <jls@stat.psu.edu>.

Maintainer:

Jing hua Zhao <jinghua.zhao@mrc-epid.cam.ac.uk>

Description:

Multiple imputation for multivariate panel or clustered data

License:

The software may be distributed free of charge and used by anyone if credit is given. It has been tested fairly well, but it comes with no guarantees and the authors assume no liability for its use or misuse.

URL:

http://www.stat.psu.edu/~jls/index.html

Reference Manual (PDF)

Name:

tdthap (Windows version)

Version:

1.1-2

Date:

2007-11-22

Title:

TDT tests for extended haplotypes

Author:

David Clayton

Maintainer:

Jing hua Zhao < jinghua.zhao@mrc-epid.cam.ac.uk>

Depends

R (>=1.5.0)

Description:

Clayton, D. and Jones, H.B. (1999), Transmission/disequilibrium tests for extended marker haplotypes, Am. J. Hum. Genet., 65:1161-1169.

License:

Artistic

URL:

http://www-gene.cimr.cam.ac.uk/clayton/software/

Reference Manual (PDF)