The RRHO package was written in collaboration with Jonathan Rosenblatt and is available as part of the Bioconductor suite to be used with the R statistical package. The package compares the degree and significance of overlap between two ranked lists of same length. The function was originally proposed by Plaisier et al. and implemented in our work (Stein et al., 2014), among others.
The CoNTExT package was written in collaboration with Luis de la Torre Ubieta in the Geschwind lab. The package evaluates the fidelity of neural stem cell differentiation. A publication describing this tools is available here (Stein et al., 2014).
The TALENSeek package was written in collaboration with Joshua Grimley at the Allen Institute for Brain Science. This tool is used to identify TALEN binding sites in the human and mouse genome. A publication describing this tool and its application is available here (Martinez et al., 2015).