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RESOURCES

SoftwarE, METHODS & MODELS
  • SpiderSeqR: R package to automate searching​ and collection of high-throughput multi-omic data-sets from NCBI SRA and GEO.
      Sozanska et al., 2020 bioRxiv
      Pirvan and Samarajiwa, 2020 bioRxiv
  • Remoat: Microarray platform re-annotation resource (website code base)
      Barbosa-Morais et al., 2009 Nuc. Acids Res.
  • Interferome: Data-resource for type I,II and III Interferon (IFN) target gene identification. Samarajiwa et al., 2009, Nuc. Acids Res.
  • Rcade: R/Bioconductor package for TF direct target identification. Collaboration With Dr Jonathan Cairns and Prof. Simon Tavaré.
      Kirschner and Samarajiwa et al., PLoS Genet. 2015
Under peer review:
  • COBRA-tft: TF direct target identification by integration of ChIP-seq datasets and RNA-seq data
  • ISGverse: A collection of reliable IFN regulated genes identified using RNA-seq data integration and a bespoke statistical method.
 

Machine & Deep Learning models:
  • EMethylNET: ML/DL model for cancer detection. Newsham et al., 2024
      GitHub: https://github.com/ss-lab-cancerunit/EMethylNet_code
      CodeOcean (platform for hosting an executable and reproducible results capsule):   https://codeocean.com/capsule/1717654/tree
      GitHub: https://github.com/ss-lab-cancerunit/MethylBoostER
      Zenodo (EU open research repository): https://zenodo.org/records/6463893
  • Piranha: ML/DL model for chromatin structure prediction. Martens et al., 2020
 
 
Coming Soon:
  • FRoGS 
  • InterferonScape 
  • Senesceome-KG
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