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Software

Packages available from Bioconductor

All Bioconductor packages can be installed by typing


> biocLite("NAME_OF_PACKAGE")

at the R prompt denoted by > .

crlmm
Description: Software for genotyping and copy number estimation from SNP arrays
Platforms: all
Maintainer: Benilton Carvalho, Matt Ritchie, and Rob Scharpf
URL: http://www.bioconductor.org/packages/release/bioc/html/crlmm.html
MergeMaid
Description: Software to facilitate multi-study analyses
Platforms: all
Maintainer: Leslie Cope and Xiaogang Zhong
URL: http://www.bioconductor.org/packages/release/bioc/html/MergeMaid.html

oligoClasses
Description: Infrastructure package for processing array data
Platforms: all
Maintainer: Benilton Carvalho and Rob Scharpf
URL: http://www.bioconductor.org/packages/release/bioc/html/oligoClasses.html

VanillaICE
Description: A hidden Markov model for inferring copy number alterations from SNP arrays
Platforms: all
Maintainer: Rob Scharpf
URL: http://www.bioconductor.org/packages/release/bioc/html/VanillaICE.html
XDE
Description: Bayesian multilevel model for cross platform differential gene expression
Platforms: all
Maintainer: Rob Scharpf URL: http://www.bioconductor.org/packages/release/bioc/html/XDE.html
MinimumDistance
Description: R package for detecting de novo copy number alterations from SNP arrays in case-parent trio designs
Platforms: all
Maintainer: Rob Scharpf
URL: https://github.com/rscharpf/MinimumDistance
hdpreg
Description: R package for Bayesian regression model with a random intercept that follows a Dirichlet Process to related random probability measures
Maintainer: Chenguang Wang and Gary Rosner
URL: Click here
BEANZ
Description: BEANZ: A Web-Based Software for Bayesian Analysis of Heterogeneous Treatment Effect in Patient-Centered Outcomes Research
Platforms: Web-Application
Maintainer: Chenguang Wang and Ravi Varadhan
URL: BEANZ

Other Software

Ochs Lab Software

APSampler
Description: Algorithm for Efficient Searches in the Space of Genetic Variation.
Maintainer: Sasha Favorov
URL: Click here.
CoGAPS
Description: Coordinated Gene Activity in Pattern Sets (CoGAPS) identifies overlapping coregulation between genes and improves inference of biological process activity.
Maintainer: Elana Fertig
URL: Click here
PattRun
Description: PattRun software permits remote and local application of algorithms that do matrix factorization.
Maintainer: Michael Ochs
URL: Click here
GESSA
Description: The Graphically Extended Stochastic Simulation Algorithm (GESSA) is a hybrid model of transcriptional reprogramming due to cell signaling.
Maintainer: Elana Fertig
URL: Click here
ONION
Description: ONION XML language is a format to encode biological relationships as prior knowledge within a Bayesian scheme.
URL: http://onion-xml.sourceforge.net
Functional Genomics Data Pipeline
Description: Utilize application server technology to permit distributed analysis....
Maintainer: Michael Ochs
URL: Click here
miRNApan
Description: R package for identifying anticorrelations in a significant subset of predicted miR - gene target expression data.
Maintainer: Michael Ochs
URL: Click here
ASAP
Maintainer: William Speier
URL: Click here
(http://cran.r-project.org/web/packages/alabama/index.html)