Some Bioconductor-oriented infrastructure for exploring transcriptional regulatory networks.
Data from studies of eQTL, DNAse footprinting and hotspot location, and sequence-based TF binding are collected in a MongoDB database.
A small example of such a database is available in a google drive. The file txreg_tiny.zip
unzips to
a folder VJCDUMP
, which is the result of a mongodump
process.
On a system with a running mongodb instance, mongorestore
can be used
with standard connection string and the path to the VJCDUMP
folder as
second argument to populate MongoDB collections for use with this package.