ENCODE Software
All software used or developed by the ENCODE Consortium
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- Distal Regulation E-G correlation — sourceCompute correlation metrics between DNase-seq signal at cCREs with DNase-seq signal at gene promoters or RNA expression levels of genes.
- Distal regulation ENCODE-rE2G — sourceTrain ENCODE-rE2G models on CRISPR enhancer screen data and apply to generate genome-wide predictions of enhancer-gene regulatory connections.
- PROcapNet Model Zoo Pipeline — sourceSoftware for BPNet models using PRO-cap data.Software type: machine learning
- TF ChIP-seq BPNet Model Zoo Pipeline — sourcePlaceholder description.Software type: machine learning
- pyrangesGenomicRanges for Python.
- pandasPandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.
- ABC-Enhancer-Gene-Prediction — sourceCell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
- EPIraction — sourceThe EPIraction algorithm uses Tikhonov-regularized least squares models to predict the interacting promoter-enhancer pairs.
- AnalyzeSpearATACSoftware used to analyze Greenleaf lab's SpearATAC (perturbation followed by snATAC-seq) data.
- CRISPRi-FlowFISHSoftware for the analysis of CRISPRi-FlowFISH data from Engreitz lab.
- GraphReg — sourceGraphReg (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.
- HiCDCPlus — sourceThe 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.
- ZeroneZerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. Publication available at: doi: 10.1093/bioinformatics/btw336
- GEM-ToolsGEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.
- Fastx Toolkit — sourceThe FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
- TRACETranscription Factor Footprinting Using DNase I Hypersensitivity Data and DNA Sequence
- bioraddbg ATAC-seq MACS2 — sourceThis 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.
- bioraddbg ATAC-seq filter beads — sourceThis 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.
- bioraddbg ATAC-seq BWA — sourceThis Docker container provides an easy to use Docker interface to the BWA alignment tool with settings tailored for Bio-Rad ATAC-Seq chemistry.
- bioraddbg ATAC-seq deconvolute — sourceThis Docker container provides an easy to use Docker interface to BAP tool with settings tailored for Bio-Rad ATAC-seq chemistry.
- guppy_basecaller — sourceOnt-Guppy is a basecalling software available to Oxford Nanopore customers. For more information, please see https://nanoporetech.com/
- polyAsite_workflow — sourcePipeline to infer poly(A) site clusters through processing of 3' end sequencing libraries prepared according to various protocols.
- gencode_utr_fix — sourceThis 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.
- interpretation_samples — sourceInterpretation code for Segway samples that produces classifier output and diagnostic plots from the apply_samples.py, for test samples.Software type: genome segmentation
- split-pipe — sourceThe 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.
- PRINSEQ Lite — sourcePRINSEQ will preprocess genomic or metagenomic sequence data in FASTA or FASTQ format
- sQTLseekeR — sourcesQTLseekeR 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 phenotypeSoftware type: variant annotation
- ggsashimi — sourcea command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments. It uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites. It is implemented in python, and internally generates R code for plotting.Software type: visualization