NEWS
TFEA.ChIP 1.15.2
New ChIP-Gene databases available
- Using ReMap2022 collections for human and mouse.
- Adding cell specific regulatory regions predicted with
ABC-Enhancer-Gene-Prediction (doi:10.1038/s41588-019-0538-0).
New Features
- New database format (older databases are still compatible). The format
consist of a list containing two elements:
- Gene Keys: vector of gene IDs
- ChIP Targets: list of vectors, one per ChIP-seq experiment,
containing the putative targets assigned. Each target is coded as
its position in the vector 'Gene Keys'.
- Database generation has been streamlined by joining together the
functions GR2tfbs_db() and makeTFBSmatrix() into one, makeChIPGeneDB().
New default database
- The TF-Gene database included with TFEA.ChIP was built using ReMap's
ChIP-seq collection (v. 2022) and GeneHancer's Double Elite regulatory
regions (v. 4.8). Because of memory limits, the internal database included
in TFEA.ChIP can only store a fraction of the 8000+ ChIP-seq experiments in
the colection. We selected the 926 ChIP-seq experiments done in ENCODE
Project's Common Cell Types.
To download the full database, as well as other ready-to-use databases
generated for TFEA.ChIP, visit:
https://github.com/LauraPS1/TFEA.ChIP_downloads