ENCODE Software

All software used or developed by the ENCODE Consortium

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  • snrna_pseudobulk — source
    Scripts for generating gene quantifications for pseudobulks.
    Software type: quantification, filtering
    Software
    released
  • subset-bam — source
    subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag.
    Software type: filtering
    Software
    released
  • Topyfic — source
    Topyfic is a Python library designed to apply rLDA to single_cells/bulk RNA-seq data to recover meaningful topics that involve the key genes like transcription factors involved in different steps.
    Software type: other
    Software
    released
  • CellBender — source
    CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
    Software type: other
    Software
    released
  • Scrublet — source
    Python code for identifying doublets in single-cell RNA-seq data.
    Software type: other
    Software
    released
  • 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
  • PROcapNet Model Zoo Pipeline — source
    Software for BPNet models using PRO-cap data.
    Software type: machine learning
    Software
    released
  • ProCapNet — source
    Software for BPNet models using PRO-cap data.
    Software type: machine learning
    Software
    released
  • TF ChIP-seq BPNet Model Zoo Pipeline — source
    Placeholder description.
    Software type: machine learning
    Software
    released
  • ATAC-seq DNase-seq ChromBPNet Model Zoo Pipeline — source
    Placeholder description.
    Software type: machine learning
    Software
    released
  • ChromBPNet — source
    ChromBPNet is a fully convolutional neural network that uses dilated convolutions with residual connections to enable large receptive fields with efficient parameterization.
    Software type: machine learning
    Software
    released
  • BPNet — source
    BPNet is a python package with a CLI to train and interpret base-resolution deep neural networks trained on functional genomics data such as ChIP-nexus or ChIP-seq.
    Software type: machine learning
    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
  • EPIraction — source
    The EPIraction algorithm uses Tikhonov-regularized least squares models to predict the interacting promoter-enhancer pairs.
    Software
    released
  • AnalyzeSpearATAC
    Software used to analyze Greenleaf lab's SpearATAC (perturbation followed by snATAC-seq) data.
    Software
    released