ENCODE Software
Software tools used in integrative analysis for the development of the Encyclopedia and SCREEN
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- SCREEN — sourceSCREEN is a web-based visualizer for the ENCODE Registry of cCREs. Users can search for cCREs by genomic region or by associated features such as genes and SNPs, and can also visualize associated underlying annotations from the ground and integrative levels of the ENCODE Encyclopedia such as gene expression, TF ChIP-seq peaks, chromatin states, and cCRE-target gene links. Additionally, users can access ENCODE data on the functional characterization of cCREs.
- ChromImpute — sourceChromImpute is software for large-scale systematic epigenome imputation. ChromImpute takes an existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally. ChromImpute bases its predictions on features from signal tracks of other marks that have been mapped in the target sample and the target mark in other samples with these features combined using an ensemble of regression trees.
- Avocado — sourceAvocado is a multi-scale deep tensor factorization method for learning a latent representation of the human epigenome. The purpose of this model is two fold; first, to impute epigenomic experiments that have not yet been performed, and second, to learn a latest representation of the human epigenome that can be used as input for machine learning models in the place of epigenomic data itself.
- vcf2diploid — sourceCreates phased diploid genomes variants from a vcf file by integrating variants to a reference genome.Software type: variant annotation
- dme-extract-se — sourceExtracts DNA-methylation from WGBS single-end alignments for ENCODE uniform processing pipeline.