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ENCODE Software

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  • Uniform Processing Pipelines
  • Consortium Analysis
All software used or developed by the ENCODE Consortium

Showing 25 of 324 results

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2550100200
  • 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
  • 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
  • psf-to-bedpe — source
    Quick script that converts psf to bedpe.
    Software
    released
  • 3d-dna — source
    We begin with a series of iterative steps whose goal is to eliminate misjoins in the input scaffolds. Each step begins with a scaffold pool (initially, this pool is the set of input scaffolds themselves). The scaffolding algorithm is used to order and orient these scaffolds. Next, the misjoin correction algorithm is applied to detect errors in the scaffold pool, thus creating an edited scaffold pool. Finally, the edited scaffold pool is used as an input for the next iteration of the misjoin correction algorithm. The ultimate effect of these iterations is to reliably detect misjoins in the input scaffolds without removing correctly assembled sequence. After this process is complete, the scaffolding algorithm is applied to the revised input scaffolds, and the output – a single “megascaffold” which concatenates all the chromosomes – is retained for post-processing.
    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
  • MaGECK — source
    Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.
    Software type: other
    Software
    released
  • RELICS — source
    RELICS is an analysis method for discovering functional sequences from tiling CRISPR screens.
    Software type: quantification
    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
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