Earlham Institute Apps

All EI apps are available within the DE (though you may experience some temporarily limitations due to the technology integration, in which case you can contact us), and run on CyVerse UK hardware.

Apps & the Testing Discovery Environment at Warwick

A full list of applications developed by the Warwick team is given in the list:
  • Sequence Alignment
    • APPLES: a set of tools to analyse promoter sequences on a genome-wide scale
  • Footprint Identification
    • Wellington Bootstrap: an algorithm for the identification of regions occupied by proteins in DNase-seq data, performing a differential analysis between two samples
    • Wellington Footprint: an algorithm for the identification of regions occupied by proteins in DNase-seq data
  • Differential Expression
    • GP2S: a differential expression algorithm for time series data with a two condition (e. g. control/treated) experimental design
    • Gradient Tool: an algorithm for the identification of the time of change from single condition time course expression data
  • Network Inference
    • CSI: a network inference algorithm capable of inferring causal regulatory network models from time course expression data
    • hCSI: an expansion of CSI network inference to handle multiple time course datasets
    • oCSI: an expansion of CSI network inference to handle data from multiple organisms
  • Clustering/Biclustering
    • BHC: a clustering algorithm for expression data originally made available in R, allows for the analysis of both time course or multiple static datasets
    • TCAP: a clustering algorithm for time course expression data, identifies complex regulatory groups thanks to a rich information measure
    • Wigwams: an algorithm for the extraction of gene groups co-regulated across subsets of multiple time course datasets
  • Transcription Factor Motif Enrichment
    • HMT: a transcription factor binding site over representation analysis algorithm for known motifs
    • MEME-LaB: a transcription factor binding site over representation analysis algorithm with novel motif discovery
NOTE: The Warwick Discovery Environment has now been discontinued. These applications are also accessible through the Warwick testing Discovery Environment. Please note this is not the same as the CyVerse DE, and is only for testing applications.

CIPRES Phylogeny Apps

CIPRES apps are supported by CyVerse UK to benefit UK users. Please see here for in depth documentation: CIPRES Phylogenetic Collection (BEAST2, MrBayes, RAxML).
  • MrBayes: Bayesian analysis of molecular sequences using MCMC
  • BEAST2: Bayesian analysis of molecular sequences using MCMC
  • RAxML: Bayesian analysis of molecular sequences using MCMC