ENCODE Software
All software used or developed by the ENCODE Consortium
Showing 12 of 12 results
Number of displayed results:
- OpenMiChrom — sourceUsed to create an ensemble of 3D structures with chromatin dynamics simulation software with input data from the Sequence Annotations (bed file) from PyMEGABASE.
- PyMEGABASE — sourcePyMEGABASE is used to generate sequence annotations at the compartment and subcompartment level for physical modeling annotations.
- 3d-dna — sourceWe begin with a series of iterative steps whose goal is to eliminate misjoins in the input scaffolds. Each step begins with a scaffold pool (initially, this pool is the set of input scaffolds themselves). The scaffolding algorithm is used to order and orient these scaffolds. Next, the misjoin correction algorithm is applied to detect errors in the scaffold pool, thus creating an edited scaffold pool. Finally, the edited scaffold pool is used as an input for the next iteration of the misjoin correction algorithm. The ultimate effect of these iterations is to reliably detect misjoins in the input scaffolds without removing correctly assembled sequence. After this process is complete, the scaffolding algorithm is applied to the revised input scaffolds, and the output – a single “megascaffold” which concatenates all the chromosomes – is retained for post-processing.
- juicertoolsSoftware package for analysis of Hi-C data.
- JuicerJuicer is a platform for analyzing high-resolution Hi-C data.
- JavaJava virtual machine