Motivation: We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression quantitative trait loci (eQTL) or Hi-C genome conformation data and reports the most likely candidate genes. In the absence of annotation data, geneAttribution relies on the distances between the genes and the input variant. Availability and Implementation: The package is freely available from http://www.bioconductor.org/ . A quick-start vignette is included with the package. Contact: [email protected].

Abstract Summary: GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R’s memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation. Availability and implementation: GWASTools is implemented in R and is available from Bioconductor (http://www.bioconductor.org). An extensive vignette detailing a recommended work flow is included. Contact: [email protected]

Clusters of microcalcifications which appear like small white grains of sand on mammograms are the earliest signs of breast cancer. In this work we employ a Gabor filter bank for texture analysis of mammograms to detect microcalcifications. A subset of the Gabor filter bank with a certain central frequency and different orientations is used to obtain the Gabor-filtered images. The filtered images are then subjected to a histogram based threshold to obtain binary images. Feature vectors are computed using the binary images. A k-means clustering algorithm with a variance scaled Euclidean distance is used for segmentation of the image.