ENCODE Software
All software used or developed by the ENCODE Consortium
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- GraphReg — sourceGraphReg (Chromatin interaction aware gene regulatory modeling with graph attention networks) is a graph neural network based gene regulation model which integrates DNA sequence, 1D epigenomic data (such as chromatin accessibility and histone modifications), and 3D chromatin conformation data (such as Hi-C, HiChIP, Micro-C, HiCAR) to predict gene expression in an informative way.
- HiCDCPlus — sourceThe package HiCDCPlus provides methods to determine significant and differential chromatin interactions by use of a negative binomial generalized linear model, as well as implementations for TopDom to call topologically associating domains (TADs), and Juicer eigenvector to find the A/B compartments. This vignette explains the use of the package and demonstrates typical workflows on HiC and HiChIP data.
- rtracklayer — sourceExtensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
- Genomic Alignments — sourceProvides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.