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.
- ABC-Enhancer-Gene-Prediction — sourceCell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
- 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.
- Library sequencing match — sourceHouse script that was matching the guides (from an input list) to the fastq files as returned by deep sequencingSoftware type: quantification
- CRISPR screen peak calling — sourceTakes CASA output and makes ENCODE sandard element quantification fileSoftware type: file format conversion
- CRISPR screen track builder — sourceTakes guide quantification and builds a browser track perturbation signal fileSoftware type: quantification
- CRADLE — sourceCRADLE (Correcting Read counts and Analysis of DifferentiaLly Expressed regions) is a package that was developed to analyze STARR-seq data. CRADLE removes technical biases from sonication, PCR, mappability and G-quadruplex sturcture, and generates bigwig files with corrected read counts. CRADLE then uses those corrected read counts and detects both activated and repressed enhancers. CRADLE will help find enhancers with better accuracy and credibility.
- mpraflow-tsv-to-bedThis is a one-line custom Perl script used to generate a bed format file from tsv.