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. [published ahead of print February 20 2021]. Nat Genet. 2021.
Original Data: 
Stowers Original Data Repository (Data Pending) | Accession ID: LIBPB-1456
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. Data used to train, evaluate and interpret the BPNet models are found on ZENODO  (https://doi.org/10.5281/zenodo.3371215). The analysis code for the manuscript is available in GitHub under the "kundajelab/bpnet-manuscript" repository (https://github.com/kundajelab/bpnet-manuscript and https://doi.org/10.5281/zenodo.4294813). The BPNet software package is available at https://github.com/kundajelab/bpnet/. The ChIP-nexus data processing pipeline is available at https://github.com/kundajelab/chip-nexus-pipeline. Software to trim and de-duplicate ChIP-nexus reads is available at https://github.com/Avsecz/nimnexus/. The BPNet model trained on ChIP-nexus data is available on Kipoi under the name "BPNet-OSKN" (http://kipoi.org/models/BPNet-OSKN/). Genome browser tracks showing observed/predicted ChIP-nexus signal and the contribution scores for all factors are available at https://genome.ucsc.edu/s/mlweilert/mesc_OSKN_tracks. 

 

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