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comparison ideas.xml @ 95:ff4d84a01fa7 draft

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author greg
date Tue, 05 Sep 2017 08:44:07 -0400
parents 7d9af0d824ad
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94:7d9af0d824ad 95:ff4d84a01fa7
235 </test> 235 </test>
236 </tests> 236 </tests>
237 <help> 237 <help>
238 **What it does** 238 **What it does**
239 239
240 IDEAS (an **I**ntegrative and **D**iscriminative **E**pigenome **A**nnotation **S**ystem) identifies de novo 240 IDEAS (an **I**\ ntegrative and **D**\ iscriminative **E**\ pigenome **A**\ nnotation **S**\ ystem) identifies
241 regulatory functions from epigenetic data in multiple cell types jointly. It is a full probabilistic model 241 de novo regulatory functions from epigenetic data in multiple cell types jointly. It is a full probabilistic
242 defined on all data, and it combines signals across both the genome and cell types to boost power. The underlying 242 model defined on all data, and it combines signals across both the genome and cell types to boost power. The
243 assumption of IDEAS is that, because all cell types share the same underlying DNA sequences, **functions of each 243 underlying assumption of IDEAS is that, because all cell types share the same underlying DNA sequences,
244 DNA segment should be correlated**. Also, cell type specific regulation is locus-dependent, and thus IDEAS uses 244 **functions of each DNA segment should be correlated**. Also, cell type specific regulation is locus-dependent,
245 local epigenetic landscape to **identify de novo and local cell type clusters** without assuming or requiring a 245 and thus IDEAS uses local epigenetic landscape to **identify de novo and local cell type clusters** without
246 known global cell type relationship. 246 assuming or requiring a known global cell type relationship.
247 247
248 IDEAS takes as input a list of epigenetic data sets (histones, chromatin accessibility, CpG methylation, TFs, etc) 248 IDEAS takes as input a list of epigenetic data sets (histones, chromatin accessibility, CpG methylation, TFs, etc)
249 or any other whole-genome data sets (e.g., scores). Currently the supported data formats include BigWig and BAM. 249 or any other whole-genome data sets (e.g., scores). Currently the supported data formats include BigWig and BAM.
250 All data sets will first be mapped by IDEAS to a common genomic coordinate in a selected assembly (200bp windows 250 All data sets will first be mapped by IDEAS to a common genomic coordinate in a selected assembly (200bp windows
251 by default, or user-provided). The user can specify regions to be considered or removed from the analysis. The 251 by default, or user-provided). The user can specify regions to be considered or removed from the analysis. The