README.md

In ManuSetty/SeqGL: Group lasso for Dnase/ChIP-seq data

SeqGL

SeqGL is a group lasso-based algorithm to extract multiple transcription factor (TF) binding signals from ChIP- and DNase-seq profiles. Benchmarked on over 100 ChIP-seq experiments, SeqGL outperformed traditional motif discovery tools in discriminative accuracy and cofactor detection. SeqGL successfully scales to DNase-seq data, identifying a large multiplicity of TF signals confirmed by ChIP, and can be used with multitask training to learn genomic-context and cell-type specific TF signals.

This repository is an R package to run SeqGL. Please refer to the vignette for installation and usage instructions. This package has been tested with R 3.2. The package and the vignette are available to download from the "Releases" tab. This package is also hosted on Bitbucket .

Citation

SeqGL manuscript is available from PLoS Computational Biology. If you use SeqGL for your work, please cite our paper.

    @article{SeqGL_2015,
            title = {SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps},
            author = {Manu Setty and Christina S Leslie},
            journal = {PLoS Computational Biology},
            year = {2015},
            month = {may},
            url = {http://dx.doi.org/10.1371/journal.pcbi.1004271},
            doi = {dx.doi.org/10.1371/journal.pcbi.1004271}
    }

ManuSetty/SeqGL documentation built on March 14, 2021, 3:18 a.m.