Software

I am the developer or major developer of the following R software packages.


  •  iSeq A Bioconductor/R package implementing Ising models and a dynamic signal profile algorithm for analysis of ChIP-seq (chromatin immunoprecipitation followed by next generation sequencing) data.   It can handle the data with and without controls and replicates.  http://www.bioconductor.org/packages/release/bioc/html/iSeq.html

  • iChip A Bioconductor/R package implementing Ising models for analysis of ChIP-chip (chromatin immunoprecipitation followed by microarray experiment).  It can be used to analyze the data generated from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen) and the data with and without controls and replicates.  http://www.bioconductor.org/packages/release/bioc/html/iChip.html


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