Vince Carey

Vince Carey

2 packages on CRAN

36 packages on Bioconductor

combinat

cran
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routines for combinatorics

affyContam

bioconductor
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structured corruption of cel file data to demonstrate QA effectiveness

ag3stat

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

altlr

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

arrayMvout

bioconductor
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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

ccleWrap

bioconductor
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structures and functions to interrogate CCLE

edxBioc

bioconductor
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Bioconductor overview for edX PHS525.4x

erma

bioconductor
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Software and data to support epigenomic road map adventures.

geeni

bioconductor
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Illustrate concepts of deployable statistical methodology using GEE solution

genetw12

bioconductor
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bioc workshop 2012: genetics of gene expression

genpb

bioconductor
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genetics of protein binding -- infrastructure and example data

GGBase

bioconductor
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infrastructure

GGtools

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

gQTLBase

bioconductor
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Infrastructure for eQTL, mQTL and similar studies.

gQTLseq

bioconductor
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testing for eQTL and like quantities with NGS-based data

gQTLstats

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

grasp2db

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

gtexLite

bioconductor
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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

gwascat

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

ior

bioconductor
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demonstrating a C-based 'stateful' fastq parser

keggorthology

bioconductor
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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.

ldblock

bioconductor
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Define data structures for linkage disequilibrium measures in populations.

MLInterfaces

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

parglms

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

parimport

bioconductor
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infrastructure and examples of parallelized filtered import

parody

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

pathRender

bioconductor
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build graphs from pathway databases, render them by Rgraphviz.

RbcBook1

bioconductor
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tools for building book

ROC

bioconductor
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utilities for ROC, with uarray focus

smoothMiner

bioconductor
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use smooth regression to investigate families of trajectories

vtpnet

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

clues

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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.

biocViews

bioconductor
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structures for vocabularies and narratives of views

iCheck

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

pdInfoBuilder

bioconductor
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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.

randPack

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

RBGL

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

rtracklayer

bioconductor
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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.