zoo.md

Model Zoo

Collection of pre-trained DeepCpG models for different datasets, which can be used to impute related datasets.

*NOTE: save models as .zip files

Smallwood et al. (2014)

• Smallwood et al. (2014)
• Protocol: scBS-Seq

Smallwood, Sébastien A., Heather J. Lee, Christof Angermueller, Felix Krueger, Heba Saadeh, Julian Peat, Simon R. Andrews, Oliver Stegle, Wolf Reik, and Gavin Kelsey. “Single-Cell Genome-Wide Bisulfite Sequencing for Assessing Epigenetic Heterogeneity.” Nature Methods 11, no. 8 (August 2014): 817–20. doi:10.1038/nmeth.3035.

Serum mESC

Models trained on 18 serum mouse embryonic stem cells (mESCs)

• DNA module
  • Motifs
• CpG module
• Joint module

2i mESC

Models trained on 12 2i mouse embryonic stem cells (mESCs)

• DNA module
  • Motifs
• CpG module
• Joint module

Hou et al. (2016)

• Hou et al. (2016)
• Protocol: scRRBS-Seq

Hou, Yu, Huahu Guo, Chen Cao, Xianlong Li, Boqiang Hu, Ping Zhu, Xinglong Wu, et al. “Single-Cell Triple Omics Sequencing Reveals Genetic, Epigenetic, and Transcriptomic Heterogeneity in Hepatocellular Carcinomas.” Cell Research 26, no. 3 (March 2016): 304–19. doi:10.1038/cr.2016.23.

HCC

Models trained on 25 human hepatocellular carcinoma cells (HCCs).

• DNA module
  • Motifs
• CpG module
• Joint module

HepG2

Models trained on 6 human heptoplastoma-derived (HepG2) cells.

• DNA module
  • Motifs
• CpG module
• Joint module

mESC

Models trained on 6 mouse embryonic stem cells (mESCs).

• DNA module
  • Motifs
• CpG module
• Joint module