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This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

SPICEY (SPecificity Index for Coding and Epigenetic activitY) is an R package designed to quantify cell-type specificity in single-cell transcriptomic and epigenomic data, particularly scRNA-seq and scATAC-seq. It introduces two complementary indices: the Gene Expression Tissue Specificity Index (GETSI) and the Regulatory Element Tissue Specificity Index (RETSI), both based on entropy to provide continuous, interpretable measures of specificity. By integrating gene expression and chromatin accessibility, SPICEY enables standardized analysis of cell-type-specific regulatory programs across diverse tissues and conditions.

This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.