Keles Research Group

Software from our group:

1) TileHGMM: Mixture modeling for genome-wide localization of transcription
factors. [vignette]

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].