ENCODE Software
All software used or developed by the ENCODE Consortium
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- 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
- 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").
- chromCor.Rscript — sourceCalculates correlation between two replicate DNase signals.Software type: quality metric
- modwt — sourceA very efficient implemenation of the the Maximal Overlap Discrete Wavelet Tranform (MODWT). See D. B. Percival and A. T. Walden (2000), Wavelet Methods for Time Series Analysis. Cambridge, England: Cambridge University Press. This is not the usual discrete wavelet transform found in, for example, gsl but an extended set of algorithms designed to overcome some problems with the usual discrete wavelet transform.
- StamPipesThis is a focused collection of makefiles and scripts to for analysis on Illumina sample data. While this probably can't be directly used by someone not in our lab, it might be a useful reference for others.Software type: filtering