ENCODE Software
All software used or developed by the ENCODE Consortium
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- CRISPR screen peak calling — sourceTakes CASA output and makes ENCODE sandard element quantification fileSoftware type: file format conversion
- dnase-densityGenerates normalized density signal from aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: file format conversion
- lrna-signalsSignal generation for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- bigWigToWig — sourceThe binary bigWig format can be converted to the text based wig or bedGraph formats using this utility.Software type: file format conversion
- rampage-signals — sourceSignal generation for Rampage ENCODE uniform processing pipeline.Software type: file format conversion
- srna-signals — sourceSignal generation for small-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- lrna-signals-unstranded — sourceSignal generation from unstranded alignments for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- lrna-signals-stranded — sourceSignal generation from stranded alignments for bulk-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
- nanostringToBed — sourceThis is a custom script to convert the results of Nanostring Nsolver from mirbase identifiers to genomic coordinates in BED and bigBED format.Software type: file format conversion
- wigToBigWig — sourceThe bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. BigWig files are created initially from wiggle (wig) type files, using the program wigToBigWig. The resulting bigWig files are in an indexed binary format. The main advantage of the bigWig files is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets bigWig is considerably faster than regular wiggle files.Software type: file format conversion
- bedToBigBed — sourcebedToBigBed takes a standard bed file or a non-standard bed file with associated .as file to create a compressed bigBed version. Description of Big Binary Indexed (BBI) files and visualization of next-generation sequencing experiment results explained by W.J. Kent, PMCID: PMC2922891.Software type: file format conversion
- bedGraphToBigWig — sourceConvert bedGraph to bigWig file. Description of Big Binary Indexed (BBI) files and visualization of next-generation sequencing experiment results explained by W.J. Kent, PMCID: PMC2922891Software type: file format conversion
- BEDTools — sourceCollectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetics: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, and VCF.Software type: file format conversion
- BEDOPS — sourcePerforms common genomic analysis tasks and offers improved flexibility, scalability and execution time characteristics over previously published packages. The suite includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives.Software type: file format conversion