Tag: Joint Analysis

JAMIE 0.91 – Joint Analysis of Multiple ChIP-chip Experiments

JAMIE 0.91

:: DESCRIPTION

JAMIE (Joint Analysis of Multiple IP Experiments) is a R package to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for sharing information across experiments. Real data tests illustrate the advantage of JAMIE over a strategy that analyzes individual datasets separately.

::DEVELOPER

Ji Lab
:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

JAMIE

:: MORE INFORMATION

Citation

Wu H. and Ji H. (2010)
JAMIE: Joint analysis of multiple ChIP-chip experiments.
Bioinformatics (2010) 26 (15): 1864-1870.

Bayesian Joint Analysis

Bayesian Joint Analysis

:: DESCRIPTION

Bayesian Joint Analysis is an approach to address the two key questions in parallel, which incorporates the information of functional annotations into expression data analysis and meanwhile infer the enrichment of functional groups.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

 Bayesian Joint Analysis 

:: MORE INFORMATION

Citation

Wang X, Chen M, Khodursky AB and Xiao G,
Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations,
Statistics in Biosciences. 2012 Nov; 4(2): 300-318

DLMM 0.0.2 – Double-layered Mixture Model for Joint Analysis of Copy Number and Gene Expression Data

DLMM 0.0.2

:: DESCRIPTION

DLMM (Double-layered Mixture Model) is a software to select copy number-associated gene expression changes in high-throughput genomics data. Copy number segmentation results and criterion-based gene selection are separately reported.

::DEVELOPER

Hyungwon Choi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

  DLMM

:: MORE INFORMATION

Citation:

H. Choi, Z.S. Qin, and D. Ghosh (2010),
A Double-layered Mixture Model for Joint Analysis of Copy Number and Gene Expression Data.
J. Comput. Biol. 17(2):1-17.

AIS 1.0 – Joint Analysis of Inter-individual Spatial and Genetic Information

AIS 1.0

:: DESCRIPTION

AIS (ALLELES IN SPACE) is a computer program for the joint analysis of inter-individual spatial and genetic information.  This program performs a variety of spatial analyses with genetic data including:  Mantel Tests, Spatial Autocorrelation Analyses, Allelic Aggregation Index Analyses (AAIA), Mommonier’s Algorithm, and “Genetic Landscape Shape” interpolations

::DEVELOPER

Mark P. Miller

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AIS

:: MORE INFORMATION

Citation:

J Hered. 2005 Nov-Dec;96(6):722-4. Epub 2005 Oct 26.
Alleles in space (AIS): computer software for the joint analysis of interindividual spatial and genetic information.
Miller MP.