README.md

In aidanmacnamara/epiChoose:

epiChoose

Data-driven selection of cell line models and epigenetic comparison across cell types

• 18/07/2017

  • Working on ATAC data

  • Current matrix lists

    • As below, have added gsk_chip_filtered, all GSK data so far (with ATAC-seq added), size = 4 x 43 x 444967

  • Looking at MDS distances for Projects 1-3.

• 12/07/2017

  • Current matrix lists

    • all_data - Blueprint + Project 1 data + some lung cell line outliers, size = 50 x 18068, generated from vignettes/project_1.R, TSSs of protein-coding genes

    • mask_data - Blueprint + Project 1/3 + ENCODE, size = 112 x 444967, generated from test/test_masking.R, all regulatory regions (defined by Ensembl multi-cell build)

    • mask_data (Aidan, local) - As above with Project 2 data added, size = 137 x 444967

  • Current status

    • Graeme (Tessella) - working with mask_data using a combination of PCA and PLS (?) to attempt to uncover an immortalisation signature

    • Nam - working with all_data using hierarchical clustering on combined data types to model the haematopoietic lineage hieraerchy

    • David - Using gene/datatype clustering to look for differential patterns between cell groups

aidanmacnamara/epiChoose documentation built on Dec. 26, 2021, 3:13 a.m.