A graphical outline describing the proposed approach and algorithms in scEpiSearch for annotation of new single-cell open-chromatin profiles and better inference of their regulatory states using the collection of available data sets of single-cell epigenomes and transcriptomes. It involves the steps named as: Epigenome and Expression Reference Data Preparation, Query Processing and Mapping, and Cross-Species and Cross-Batch Query embedding. The cross-species and cross-batch query embedding represents the coembedding of multiple open-chromatin profiles irrespective of differences in peak list in the read-count matrix, batch effect, and species using existing reference single-cell profiles.