Name
Title | ||
|---|---|---|
MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates. |
Abstract | ||
|---|---|---|
Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. The robust identification of ChIP-enriched regions is frequently complicated by noisy measurements. This identification can be improved by accounting for dependencies between adjacent probes on chromosomes and by modeling of biological replicates.MultiChIPmixHMM is a user-friendly R package to analyse ChIP-chip data modeling spatial dependencies between directly adjacent probes on a chromosome and enabling a simultaneous analysis of replicates. It is based on a linear regression mixture model, designed to perform a joint modeling of immunoprecipitated and input measurements.We show the utility of MultiChIPmixHMM by analyzing histone modifications of Arabidopsis thaliana. MultiChIPmixHMM is implemented in R and including functions in C, freely available from the CRAN web site: http://cran.r-project.org. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1186/1471-2105-14-271 | BMC Bioinformatics |
Keywords | Field | DocType |
algorithms,bioinformatics,microarrays | Biology,Histone,Tiling array,ChIP-sequencing,Chip,Bioinformatics,Chromatin immunoprecipitation,Chromatin,Genetics,DNA microarray,R package | Journal |
Volume | Issue | ISSN |
14 | 1 | 1471-2105 |
Citations | PageRank | References |
5 | 0.34 | 3 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Caroline Bérard | 1 | 16 | 1.53 |
| Michael Seifert | 2 | 5 | 0.34 |
| Tristan Mary-Huard | 3 | 81 | 8.45 |
| Marie-Laure Martin-Magniette | 4 | 71 | 6.47 |