Bayesian Relevance Networks

Matlab code for our Bayesian Relevance Networks approach can be found here. R-code can be found here.

Bayesian Correlation Analysis for High Throughput Sequencing Data

R-code for our Bayesian correlation analysis method, published in PLoS ONE, is here.

Learning-Based Interactive Segmentation using the Maximum Mean Cycle Weight Formalism

Software in support of a submitted manuscript named above can be found here in zip format.

Scaling of Random Walks on Networks

Here we provide software for analyzing random walks on networks.

Adaptive-bandwidth kernel density estimation for high-throughput sequencing data

Both Matlab and R versions are available here.

FiloDetect

FiloDetect is an image analysis program for detecting and quantifying filopodia in single-cell fluorescence confocal microscopy images. The distribution package is here.

MaSC: Mappability-Sensitive Cross-Correlation

A Perl implementation of our MaSC approach to estimating fragment length from short-read high-throughput sequencing data can be found here.

State Sequence Analysis

R and Matlab software for State Sequence Analysis, an approach to analyzing the dynamics of continuous-time Markov chains, along with scripts analyzing several specific domains, can be found here.

BIDCHIPS: Bias-Decomposition of ChIP-seq Signals

A software for quantifying and Removing Biases in ChIP-Seq Signals

• The R package implementation of BIDCHIPS
• Example data for BIDCHIPS analysis from the whole human genome (hg19) and chromosome 22.
• The MATLAB version of BIDCHIPS is available here.