ENCODE Software
All software used or developed by the ENCODE Consortium
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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
- CAGT (Clustering AGgregation Tool) — sourceDeciphers the heterogeneity and diversity of profiles of functional signals (e.g., chromatin mark ChIP-seq signal) centered at a collection of sites (e.g., TSSs or TF binding sites) in a genome. Rather than averaging the profiles over all the anchor sites (traditional aggregation plots), CAGT accounts for the inherent heterogeneity in signal magnitude, shape and implicit strand orientation of chromatin marks. CAGT partitions the set of anchor sites into compact clusters such that each cluster represents anchor points that show similar patterns of the functional signal profiles with different clusters having distinct patterns. The different groups of patterns are often enriched for distinct biological functions (PMID: 22955985).Software type: genome segmentation
- 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