EpiGeEC is designed to compare and annotate a user’s epigenomic datasets using thousands of public datasets in few minutes. It can also be used to directly compare a user’s datasets. The manuscript describing epiGeEC is under review (Laperle et al.) but epiGeEC has already been used and cited in two of the recent IHEC publications (Data Portal) and (eFORGE), and is used to precalculate the correlation data on the IHEC Data Portal.
Note that the server hosting epiGeEC is limited. Please contact epiGeEC support for more information.
The source code is available here.
1) Use the epiGeEC Public Dataset Selection tool to identify the public datasets of interest among the ~8000 from IHEC hg19, ~3000 from IHEC hg38, ~150 from IHEC mm10 and ~1000 yeast from GEO and mapped onto sacCer3.
2) Use epiGeEC Correlation Matrix to calculate the Pearson correlation score between each pair of the selected datasets (which can also include private datasets).
3) Use epiGeEC Annotate Matrix on the output of the first two tools to generate a PDF report in addition to a tabular (TSV) file containing the metadata of each dataset. The PDF contains a hierarchical clustering heatmap representation annotated with pie charts based on the provided metadata, as well as a multidimensional scaling (MDS) representation of the datasets.
4) Use epiGeEC Evaluate Clustering to evaluate how well the structure of the clusters corresponds to the provided metadata for each category of labels by calculating the Adjusted Rand Index (ARI) score for different categories and sub-categories of metadata.
This epiGeEC Galaxy instance is provided by the Genetics and genomics Analysis Platform (GenAP) hosted within the Calcul Québec and Compute Canada infrastructure, and developped by a team from the CCS at the Universite de Sherbrooke, and from the Mcgill University and Mcgill University and Genome Quebec Innovation Center (MUGQIC)
