ENCODE Software
Software tools implemented and developed by the consortium for computational analysis
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- interpretation_samples — sourceInterpretation code for Segway samples that produces classifier output and diagnostic plots from the apply_samples.py, for test samples.Software type: genome segmentation
- Genomedata — sourceEfficiently stores multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. Utilities have also been developed to load data into this format. A reference implementation in Python and C components is available under the GNU General Public License.
- Segway — sourceUses a machine learning method to analyze multiple tracks of functional genomics data, searching for recurring patterns. The software automatically partitions the genome into non-overlapping segments and assigns each segment a label. The resulting annotation provides a human-interpretable summary of the functional landscape of the genome, yielding hypotheses about novel instances or classes of functional elements.Software type: genome segmentation
- Segtools — sourceA Python package that analyzes genomic segmentations. The software efficiently calculates a variety of summary statistics and produces corresponding publication quality visualizations. The overall goal of Segtools is to provide a bird's-eye view of complex genomic data sets, allowing researchers to easily generate and confirm hypotheses.Software type: genome segmentation