ENCODE Software
All software used or developed by the ENCODE Consortium
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- mex_gene_archive — sourcemex_gene_archive is a minimal file format designed to meet the needs of archiving sparse gene matrices in a format compatible with the ENCODE 4 Data Coordination Center.Software type: other
- OpenMiChrom — sourceUsed to create an ensemble of 3D structures with chromatin dynamics simulation software with input data from the Sequence Annotations (bed file) from PyMEGABASE.
- PyMEGABASE — sourcePyMEGABASE is used to generate sequence annotations at the compartment and subcompartment level for physical modeling annotations.
- SwanSwan is a Python library designed for the analysis and visualization of transcriptomes.Software type: other
- CerberusCerberus software for long-read RNA-seq analysisSoftware type: other
- 3d-dna — sourceWe 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.
- eFORGE — sourceeFORGE identifies tissue or cell type-specific signal by analysing a minimum set of 5 differentially methylated positions (DMPs) for overlap with DNase I hypersensitive sites (DHSs) compared to matched background DMPs and provides both graphical and tabulated outputs.Software type: integrated analysis
- encode_utils — sourceTools that are useful to any ENCODE Consortium submitting group, as well as the general community working with ENCODE data. Library and scripts are coded in Python.
- eCLIP core pipeline — sourceCustom software developed by Yeo lab for use in the eCLIP pipeline.Software type: other
- Bru-seq ToolsThe Ljungman lab scripts used to process Bru-seq, BruUV-seq, and BruChase data.
- Vierstra digital genomic footprinting — sourcefootprint-tools is a python module for de novo detection of genomic footprints from DNase I data by simulating expected cleavage rates using a 6-mer DNase I cleavage preference model combined with density smoothing. Statistical significance of per-nucleotide cleavages are computed from a series emperically fit negative binomial distribution.
- Altius Index — sourceMethod for generating a master list / Index of DNaseI-Hypersensitive Sites ("consensus DHSs").