ENCODE Software

All software used or developed by the ENCODE Consortium

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  • Distal Regulation E-G correlation — source
    Compute correlation metrics between DNase-seq signal at cCREs with DNase-seq signal at gene promoters or RNA expression levels of genes.
    Software
    released
  • FUNCODE — source
    Scripts for computing Functional Conservation of DNA Elements (FUNCODE) scores from ENCODE DNase-seq, ATAC-seq and Histone ChIP-seq data
    Software
    released
  • Distal regulation ENCODE-rE2G — source
    Train ENCODE-rE2G models on CRISPR enhancer screen data and apply to generate genome-wide predictions of enhancer-gene regulatory connections.
    Software
    released
  • mex_gene_archive — source
    mex_gene_archive is a minimal file format designed to meet the needs of archiving sparse gene matrices in a format compatible with the ENCODE 4 Data Coordination Center.
    Software type: other
    Software
    released
  • CNDBTools — source
    Used to generate the in-silico Hi-C map for each chromosome.
    Software
    released
  • OpenMiChrom — source
    Used to create an ensemble of 3D structures with chromatin dynamics simulation software with input data from the Sequence Annotations (bed file) from PyMEGABASE.
    Software
    released
  • PyMEGABASE — source
    PyMEGABASE is used to generate sequence annotations at the compartment and subcompartment level for physical modeling annotations.
    Software
    released
  • pyranges
    GenomicRanges for Python.
    Software
    released
  • pandas
    Pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.
    Software
    released
  • Swan
    Swan is a Python library designed for the analysis and visualization of transcriptomes.
    Software type: other
    Software
    released
  • seqFISH+ — source
    Pipeline to process seqFISH data.
    Software type: quantification, other
    Software
    released
  • ABC-Enhancer-Gene-Prediction — source
    Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
    Software
    released
  • AnalyzeSpearATAC
    Software used to analyze Greenleaf lab's SpearATAC (perturbation followed by snATAC-seq) data.
    Software
    released
  • gRNA_to_log2FC — source
    Script for computing log2fc bigwig from gRNA counts
    Software
    released
  • GT_Scan — source
    GT-Scan is a web-based tool that scans a user-defined genomic region for candidate targets and ranks them in terms of the number of exact or approximate off-targets in the genome.
    Software
    released
  • Cerberus
    Cerberus software for long-read RNA-seq analysis
    Software type: other
    Software
    released
  • LAPA — source
    Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
    Software type: other
    Software
    released
  • CRISPRi-FlowFISH
    Software for the analysis of CRISPRi-FlowFISH data from Engreitz lab.
    Software
    released
  • CRISPy — source
    CRISPy is a lightweight versatile pipeline for CRISPR-screening analysis.
    Software type: quantification
    Software
    released
  • GraphReg — source
    GraphReg (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.
    Software
    released
  • HiCDCPlus — source
    The 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.
    Software
    released
  • Zerone
    Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. Publication available at: doi: 10.1093/bioinformatics/btw336
    Software
    released
  • GEM-Tools
    GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.
    Software
    released
  • Fastx Toolkit — source
    The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
    Software
    released
  • TRACE
    Transcription Factor Footprinting Using DNase I Hypersensitivity Data and DNA Sequence
    Software
    released