MIRA

:: DESCRIPTION

The MIRA package aggregates DNA methylation across the genome for instances of a genomic feature like histone ChIP peaks, transcription factor ChIP peaks, or open chromatin regions in order to give a single signature and score for that feature, which may be used to infer regulatory activity.

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation

Lawson JT, Tomazou EM, Bock C, Sheffield NC.
MIRA: an R package for DNA methylation-based inference of regulatory activity.
Bioinformatics. 2018 Aug 1;34(15):2649-2650. doi: 10.1093/bioinformatics/bty083. PMID: 29506020; PMCID: PMC6061852.

DeepArk

:: DESCRIPTION

DeepArk is a set of deep learning algorithms capable of predicting regulatory activity (e.g. transcription factor binding) from genomic sequences. DeepArk consists of four distinct neural networks for mouse (Mus musculus), fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and zebrafish (Danio rerio)

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

DeepArk: modeling cis-regulatory codes of model species with deep learning

Evan M. Cofer, João Raimundo, Alicja Tadych, Yuji Yamazaki, Aaron K. Wong, Chandra L. Theesfeld, Michael S. Levine, Olga G. Troyanskaya

bioRxiv 2020.04.23.058040; doi: https://doi.org/10.1101/2020.04.23.058040

Tag: Regulatory Activity

MIRA – Methylation-based Inference of Regulatory Activity

MIRA

DeepArk – Deep Learning models of Regulatory Activity for Model Species

DeepArk