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Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec Z, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Nat Genet. 2021;53:354-366.

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Stowers Original Data Repository | Accession ID: LIBPB-1456
<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137193" target="_blank" rel="noopener nofollow noreferrer">NCBI GEO | Accession No: GSE137193</a>&nbsp;<div>GITHUB:<a href="https://github.com/kundajelab/bpnet-manuscript" target="_blank" rel="noopener nofollow noreferrer"> kundajelab/bpnet-manuscript</a>; <a href="https://github.com/kundajelab/bpnet" target="_blank" rel="noopener nofollow noreferrer">kundajelab/bpnet;</a> <a href="https://github.com/kundajelab/chip-nexus-pipeline" target="_blank" rel="noopener nofollow noreferrer">kundajelab/chip-nexus-pipeline</a>; <a href="https://github.com/kundajelab/nimnexus" target="_blank" rel="noopener nofollow noreferrer">kundajelab/nimnexus</a>&nbsp;</div><div><a href="https://doi.org/10.5281/zenodo.4294813" target="_blank" rel="noopener nofollow noreferrer">Zenodo 4294813&nbsp;</a></div><div><a href="https://doi.org/10.5281/zenodo.3371215" target="_blank" rel="noopener nofollow noreferrer">Zenodo 3371215</a></div><div><a href="https://genome.ucsc.edu/s/mlweilert/mesc_OSKN_tracks" target="_blank" rel="noopener nofollow noreferrer">UCSC</a></div><div><u><span><a href="http://kipoi.org/models/BPNet-OSKN/" target="_blank" rel="noopener nofollow noreferrer">Kipoi</a></span></u></div>

Publication Notes

The Stowers Institute contributing authors have selected to present the raw data of this manuscript resulting from work performed at The Stowers Institute. Data sets have been deposited in GEO under the accession number GSE137193.&nbsp;Data used to train, evaluate and interpret the BPNet models are found on ZENODO.&nbsp;The analysis code for the manuscript is available in GitHub under the "kundajelab/bpnet-manuscript" repository.&nbsp;The BPNet software package is available at GITHUB.&nbsp;The ChIP-nexus data processing pipeline is available at&nbsp;GITHUB. Software to trim and de-duplicate ChIP-nexus reads is available at&nbsp;<a href="https://github.com/Avsecz/nimnexus/" target="_blank" title="https://github.com/avsecz/nimnexus/" rel="noopener nofollow noreferrer">GITHUB</a>.&nbsp;The BPNet model trained on ChIP-nexus data is available on Kipoi under the name "BPNet-OSKN". Genome browser tracks showing observed/predicted ChIP-nexus signal and the contribution scores for all factors are available at&nbsp;Kipoi.

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