This page collects released software packages.
The results in papers are generated by analysis scripts that are separate from released and carefully documented software packages. It may not be as pretty, or unit tested, or documented, but nonetheless, in an effort towards best reproducible research, we are trying to release the code supporting published results. Where available, these will be linked from the individual papers.

R packages

To install R packages directly from github, do, in R:

install.packages("devtools")
library(devtools)
install_github("chr1swallace/package.name")

coloc

package website // CRAN // github // A package of R functions used to test for colocalisation of two genetic traits. For more detail or the statistical background and applications see: (1) (2).

New in v3.1 which is now up to date on CRAN: finemap.abf() offers finemapping of single traits under a single causal variant assumption. See vignette for details.

GUESSFM

package website // github // A wrapper around the GUESS stochastic model search method for fine mapping causal variants in genetic data. See (missing reference) more detail here.

simGWAS

package website // github // Fast and accurate simulation of case-control GWAS summary statistics (missing reference)

colocCommonControl

CRAN // github // Adaptation of coloc for comparing two GWAS studies which share controls (3).

annotSnpStats

github // extends SnpMatrix objects from the snpStats package by tying in sample and snp annotation data.frames. It allows the joint manipulation, and binding, of such objects, and includes a few functions I use for finding duplicate samples, applying QC, and aligning alleles between different datasets. It seems to work, and I intend to push it to CRAN in the future.

snpStatsWriter

github // allows writing snpStats objects to disk in formats suitable for reading by snphap, phase, mach, IMPUTE, beagle, and (almost) anything else that expects a rectangular format.

wgsea

CRAN // implements a Wilcoxon-based test for Gene Set Enrichment Analysis when testing regions of the genome according to GWAS derived evidence for SNP-trait association. For more detail, see the supplementary methods of (4).

extraBinomial

CRAN // (author Xin Yang, listed here because Xin doesn’t have her own website) uses an extra binomial model to test for case-control allele frequency differences in pooled sequence data (5).

origin

github // implements an extension to the Weinberg method for testing for parent of origin effects to allow for multiple affected offspring in a nuclear family. I haven’t used it in a while, and it requires some checking just to get it to pass the CRAN tests. Unless I need to revisit it for another reason, I am unlikely to push it to CRAN, but it is a finished package. For more detail see:

Weinberg et al. Methods for detection of parent-of-origin effects in genetic studies of case-parents triads. /Am J Hum Genet/ 65:229-235. 1999.

Wallace et al. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. /Nat Genet/ 2010. [ Europe PMC ]

Non-R packages

VSEAMS (Olly Burren)

Variant set enrichment analysis (of association summary statistics) using multivariate sampling. Please see the wiki available at this wiki for further details. Method described in (6).