diffReps¶
Description¶
ChIP-seq is now widely used to profile the protein DNA interactions on a genome. It is of high interest to compare the differential enrichment of a histone mark or transcription factor between two contrasting conditions, such as disease vs. control. diffReps is developed to serve this purpose. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especially for in vivo brain tissues.
Environment Modules¶
Run module spider diffreps to find out what environment modules are available for this application.
Environment Variables¶
- HPC_DIFFREPS_DIR - installation directory
- HPC_DIFFREPS_BIN - executable directory
Citation¶
If you publish research that uses diffreps you have to cite it as follows:
Shen L, Shao N-Y, Liu X, Maze I, Feng J, et al. (2013) diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates. PLoS ONE 8(6): e65598. doi:10.1371/journal.pone.0065598 [Shen L, Shao N-Y, Liu X, Maze I, Feng J, et al. (2013) diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates. PLoS ONE 8(6): e65598. [1]
Categories¶
biology