March 14th, 2011 by sunduz
Software from our group:
1) TileHGMM: Mixture modeling for genome-wide localization of transcription
2) CMARRT: A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. [vignette][windows version]
2) spls: Sparse partial least squares. [vignette][Available in CRAN].
3) NucDe: A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions from MNase-chip and MNase-seq data. [vignette]
4) SUCcESS: Integrating quantitative information from ChIP-chip experiments into motif finding. [vignette]
5) MOSAiCS: Model-based one- and two-sample analysis and inference for ChIP-seq data. [Available in Bioconductor][Google Page for MOSAiCS][Available in Galaxy Tool Shed (check MOSAiCS under “Sequence Analysis” or “Statistics”].
6) Our multi-reads software for “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-seq data“ now on Galaxy Tool Shed. Check csem under “Next Gen Mappers”. Visit here for a stand alone version and more details.
7) NCIS: Normalization for ChIP-seq experiments. Manuscript ” Normalization of ChIP-seq data with control” is under review.
DBChIP: Detecting differential binding of transcription factors with ChIP-seq. [Available in Bioconductor].
Posted in News |