Vince Carey

routines for combinatorics

structured corruption of cel file data to demonstrate QA effectiveness

explorations of statistical software design in which algorithms can be written and deployed without strong assumptions about data source, data representation, or execution environment

program for regression analysis of clustered binary response, with particular attention to regression analysis of pairwise odds ratio analysis

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate

structures and functions to interrogate CCLE

Bioconductor overview for edX PHS525.4x

Software and data to support epigenomic road map adventures.

Illustrate concepts of deployable statistical methodology using GEE solution

bioc workshop 2012: genetics of gene expression

genetics of protein binding -- infrastructure and example data

infrastructure

software and data for analyses in genetics of gene expression and/or DNA methylation

Infrastructure for eQTL, mQTL and similar studies.

testing for eQTL and like quantities with NGS-based data

computationally efficient analysis of eQTL, mQTL, dsQTL, etc.

grasp2db, sqlite wrap of NHLBI GRASP 2.0, an extended GWAS catalog

This package provide sharded storage for gtex eqtl results, reduced to 500k radius per gene on 17q12 or in reactome pathway for PI3K-AKT signaling in cancer

Represent and model data in the EMBL-EBI GWAS catalog.

demonstrating a C-based 'stateful' fastq parser

graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.

Define data structures for linkage disequilibrium measures in populations.

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

support for parallelized estimation of GLMs/GEEs, catering for dispersed data

infrastructure and examples of parallelized filtered import

routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics

build graphs from pathway databases, render them by Rgraphviz.

tools for building book

utilities for ROC, with uarray focus

use smooth regression to investigate families of trajectories

variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828

We developed the clues R package to provide functions for automatically estimating the number of clusters and getting the final cluster partition without any input parameter except the stopping rule for convergence. The package also provides functions to evaluate and compare the performances of partitions of a data set both numerically and graphically.

structures for vocabularies and narratives of views

QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.

Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.

A suite of classes and functions for randomizing patients in clinical trials.

A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.