[Bioc-devel] new version with extensive updates: mosaics

Dongjun Chung chungdon at stat.wisc.edu
Fri Feb 17 22:40:20 CET 2012

Hi all,

We would like to announce a new version of our package, mosaics 
(MOdel-based one and two Sample Analysis and Inference for ChIP-Seq), 
with extensive updates.

R package mosaics implements MOSAiCS, a statistical framework for the 
analysis of ChIP-seq data, proposed in Kuan et al. (2011), JASA, 106: 
891-903. MOSAiCS stands for "MOdel-based one and two Sample Analysis and 
Inference for ChIP-Seq Data". It implements a flexible parametric 
mixture modeling approach for detecting peaks, i.e., enriched regions, 
in one-sample (ChIP sample) or two-sample (ChIP and control samples) 
ChIP-seq data. It accounts for mappability and GC content biases that 
arise in ChIP-seq data.

This new version of the mosaics package (ver 1.2.5) provides many new 
features and improvements, including:

- New model for deeply sequenced ChIP-Seq data.
- Supports for various aligned read file formats (eland_result, 
eland_extended, eland_export, bowtie, SAM, BED, CSEM).
- Preprocessing of aligned read files can be done within the R 
environment using constructBins().
- Easier model fitting for the two sample analysis using mosaicsRunAll().
- Preprocessing and model fitting become much faster (Rcpp).
- Parallel processing is now supported (multicore).

Please check the vignette of the package and 'package?mosaics' for 
further details. The package is available at 

Please post any questions or comments at our mosaics google group 
(http://groups.google.com/group/mosaics_user_group). Any comments or 
suggestions would be very helpful.


PhD Candidate
Department of Statistics
Univerisity of Wisconsin at Madison

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