ENCODE Software

All software used or developed by the ENCODE Consortium

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  • 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
  • chromVar — source
    chromVAR is an R package for the analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.
    Software
    released
  • bioraddbg ATAC-seq MACS2 — source
    This Docker container provides an easy to use Docker interface to MACS2 for peak calling with settings tailored for Bio-Rad Single Cell ATAC-seq chemistry.
    Software
    released
  • bioraddbg ATAC-seq filter beads — source
    This Docker container provides an easy to use Docker interface to a bead filtration tool with settings tailored for Bio-Rad Single Cell ATAC-seq chemistry. This container takes in .BAM files and performs "knee calling" to compute a bead barcode whitelist and jaccard index threshold for bead-to-droplet merging.
    Software
    released
  • bioraddbg ATAC-seq BWA — source
    This Docker container provides an easy to use Docker interface to the BWA alignment tool with settings tailored for Bio-Rad ATAC-Seq chemistry.
    Software
    released
  • bioraddbg ATAC-seq deconvolute — source
    This Docker container provides an easy to use Docker interface to BAP tool with settings tailored for Bio-Rad ATAC-seq chemistry.
    Software
    released
  • guppy_basecaller — source
    Ont-Guppy is a basecalling software available to Oxford Nanopore customers. For more information, please see https://nanoporetech.com/
    Software
    released
  • polyAsite_workflow — source
    Pipeline to infer poly(A) site clusters through processing of 3' end sequencing libraries prepared according to various protocols.
    Software
    released
  • gencode_utr_fix — source
    This package fixes UTR features in the third columns of Gencode GTF by converting UTR annotation into five_prime_utr and three_prime_utr similar to Ensembl.
    Software
    released
  • pyfaidx — source
    This python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index.
    Software
    released
  • seqkit — source
    A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
    Software
    released
  • STARsolo — source
    STARsolo is a tool for mapping, demultiplexing, and quantification for single cell RNA-seq.
    Software
    released
  • HTSlib — source
    A C library for reading/writing high-throughput sequencing data
    Software
    released
  • fastp — source
    Tool for preprocessing fastq files
    Software
    released
  • ArchR — source
    R package for single-cell ATAC-seq data analysis
    Software
    released
  • Scanpy — source
    Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing.
    Software
    released
  • LR-splitpipe — source
    Demultiplexing and debarcoding tool designed for LR-Split-seq data.
    Software
    released
  • Seurat — source
    Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
    Software
    released
  • split-pipe — source
    The Parse Biosciences computational pipeline is an out-of-the-box software tool that you can run locally to convert fastq files straight to processed data (including gene-cell count matrices). Customers purchasing the Whole Transcriptome Kit will receive access to the Parse computational pipeline.
    Software
    released
  • PINTS — source
    Yu lab repository for signal generation and peak calling scripts
    Software
    released
  • dREG — source
    Detecting Regulatory Elements using GRO-seq and PRO-seq
    Software
    released
  • bigWigMerge — source
    This tool from kentUtils merges together multiple bigWigs into a single output
    Software
    released
  • PRINSEQ Lite — source
    PRINSEQ will preprocess genomic or metagenomic sequence data in FASTA or FASTQ format
    Software
    released
  • sQTLseekeR — source
    sQTLseekeR is a package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. In sQTLSeeker, splicing patterns are modeled by the relative expression of the transcripts of a gene. The most recent version of sQTLseekeR can be employed to detect genetic variant associated to any multivariate phenotype
    Software type: variant annotation
    Software
    released